I turn on the ignition, and put the vehicle in reverse or drive, the door locks will go click-click. When I turn off and tried to close the doors(beeper),the doors lock, but the alarm don't activate

I've had a strange issue with my drivers door the last week. I go out and unlock my door with wireless clicker. Then I reach in put the key in the ignition start the truck, make sure the defrost is on. Then I step away and slam the door, 'bump',,, I look back, the door did not click shut, again I slam the door 'bump'..it does not click shut. Bump Bump Bump...I try to shut it...then I reach in and push the lock/unlock button , lock/unlock...lock/unlock...on the door..click..click...it does beep or the horn toots..remember trucks key is in ignition , truck running, and I'm clicking the button on the inside of the door. Finally the door will shut and hold closed , once it was not locked,,,once it was shut and locked. I had to get my other set of keys to unlock the door.

LOCKING AND UNLOCKING
You can use the power door lock control or the remote control to lock and unlock your doors and tailgate.See Tailgate Lock.
Power Door Locks
The power door lock control is on the driver and front passenger door panels.

AUnlock.
BLock. Remote Control
You can use the remote control at any time your vehicle is not running.
Unlocking the Vehicle (Two-Stage Unlock)
Press the button to unlock the driver door. Press the button again within three seconds to unlock all doors.The direction indicators flash. The direction indicators flash twice to confirm the change. The unlocking mode applies to the remote control, keyless entry keypad and intelligent access.
Press and hold both the lock and unlock buttons on the remote control for four seconds to disable or enable two-stage unlocking. Disabling two-stage unlocking allows your entire vehicle to unlock with one press of the button.
Intelligent access at the driver door unlocks your entire vehicle when you disable two-stage unlocking.
Locking the Vehicle
Press the button to lock all doors.The direction indicators flash.
Press the button again within three seconds to confirm that all the doors are closed.The doors lock again, the horn sounds and the direction indicators flash if all the doors are closed.
Mislock
If any door is open, or if the hood is open on vehicles with an anti-theft alarm or remote start, the horn sounds twice and the direction indicators do not flash.
Activating Intelligent Access
General Information
You can unlock and lock the vehicle without taking the keys out of your pocket or purse when your intelligent access key is within 3 ft (1 m) of your vehicle. Intelligent access uses a sensor on the back of the door handle for unlocking and a separate sensor on the face of each door handle for locking.
The system does not function if:

• Your vehicle battery has no charge.
• The key battery has no charge.
• The key frequencies are jammed.

Note: The system may not function if the key is close to metal objects or electronic devices, for example keys or a cell phone.
Note: If the system does not function, use the key blade to lock and unlock your vehicle. See Remote Control.
Unlocking Using Intelligent Access
With your intelligent access key within 3 ft (1 m) of your vehicle, touch the unlock sensor on the back of the door handle for a brief period and then pull on the door handle to unlock, being careful to not touch the lock sensor at the same time or pulling the door handle too quickly. The intelligent access system requires a brief delay to authenticate your intelligent access key fob.
Locking Using Intelligent Access
With your intelligent access key within 3 ft (1 m) of your vehicle, touch the outer door handle lock sensor for approximately one second to lock, being careful to not touch the unlock sensor on the back of the door handle at the same time. After locking, you can immediately pull on the door handle to confirm locking occurred without inadvertently unlocking.
Note: Do not use the outside door handle as a roof cargo strap.
At the Electronic Tailgate (If Equipped)
Press the exterior tailgate release button inside of the tailgate handle. The tailgate unlocks and opens. See Electronic Tailgate.
Smart Unlock
This feature helps to prevent you from locking your intelligent access key inside your vehicle's passenger compartment or rear cargo area.
If you leave your key in the ignition, when you open the driver door and lock your vehicle with the power door lock control, the doors lock then unlock.
You can still lock your vehicle with the key in the ignition by:

• Using the manual lock on the inside of the door.
• Locking the driver door with a key.
• Using the keyless entry keypad.
• Using the lock button on the remote control.

Smart Unlocks for Intelligent Access Keys
This feature helps to prevent you from locking your intelligent access key inside your vehicle's passenger compartment or rear cargo area.
When you lock your vehicle using the power door lock control (with the door open, vehicle in park and ignition off), your vehicle searches for an intelligent access key in the passenger compartment after you close the door. If your vehicle finds a key, all of the doors immediately unlock.
In order to override the smart unlock feature and intentionally lock the intelligent access key inside your vehicle, you can lock your vehicle after all doors are closed by using the keyless entry keypad, pressing the lock button on another intelligent access key or touching the locking area on the handle with another intelligent access key in your hand.
When you open one of the front doors and lock your vehicle using the power door lock control, all doors lock then unlock if the ignition is on.
Autolock
Autolock locks all the doors when:

• All doors are closed.
• The ignition is on.
• You shift into any gear putting your vehicle in motion.
• Your vehicle reaches a speed greater than 12 mph (20 km/h).

Autolock repeats when:

• You open then close any door while the ignition is on and your vehicle speed is 9 mph (15 km/h) or lower.
• Your vehicle reaches a speed greater than 12 mph (20 km/h).

Autounlock
Autounlock unlocks all the doors when:

• The ignition is on, all the doors are closed, and your vehicle has been moving at a speed greater than 12 mph (20 km/h).
• Your vehicle comes to a stop and you switch the ignition off or to the accessory position.
• You open the driver door within 10 minutes of switching the ignition off or to accessory.

Note: The doors do not autounlock if you electronically lock your vehicle after you switch the ignition off and before you open the driver door.
Enabling or Disabling Autounlock
You can enable or disable the autounlock feature in the information display or an authorized dealer can do it for you. See General Information.
Illuminated Entry
The interior lamps and select exterior lamps illuminate when you unlock the doors with the remote entry system.
The illuminated entry system turns off the lights if:

• The ignition is on.
• You press the remote control lock button.
• After 25 seconds of illumination.

The dome lamp does not turn on if the control is set to the off position.
The lights do not turn off if:

• You switch them on with the dimmer control.
• Any door is open.

Battery Saver
The battery saver turns off the interior lamps 30 minutes after you switch off the ignition if a door is open and the dome lamp switch is on. It turns off the interior lamps after 10 minutes if the dome lamp switch is off.
Accessory Mode Battery Saver for Intelligent Access Keys (If Equipped)
If you leave the ignition on after leaving your vehicle, it turns off 15 minutes after you close all of the doors.

The clicking you hear is the vehicle asking for the program sequence to reprogram the locking system. Apparently something threw it out of sequence, ( a battery change , jumpstart, voltage spike , etc). The programming sequence that mazda uses is really kinda crazy. I was able to locate the sequence to try. If it does not work have the dealership flash the pcm, (another word for reprogram the powertrain control module). Here is the sequence:
1) Get in MPV with ignition key, and all fobs for the vehicle.
2) Close all doors and remove ignition key if it is in ignition.
3) Open driver's door
Note: Steps 4 and 5 must be completed in under thirty seconds.
4) Repeat the following three times
a) Insert ignition key
b)Turn ignition switch to on and then to lock
c) Remove ignition key
5) Repeat the following three times
a) Close driver's door
b) Open driver's door
Locks should all lock and then unlock within a couple of seconds--you'll hear the clicking sound
6) Press any button two times within five seconds on fob being programmed.
Locks should again lock and unlock
7) Repeat step 6 for all other fobs being programmed. When done with last fob, wait a few seconds and then you should be done with the reprogramming. Each fob should now work for this vehicle.

Here are the instructions for programming the 99-02 4Runner Keyless Entry factory remotes:

1. Start with the following conditions: you are in the vehicle

a. Key is out of the ignition
b. Drive door is open ( all other doors are closed)
c. Driver door is unlocked (other door locks don't matter)

2. Insert the key into the ignition (don't turn it) and pull it out.

3. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times. Use an even pace and try
to go relatively fast.

b. Close, then open the drivers door.

4. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times (same as before).
b. Turn the ignition to ON then back to OFF.
c. Turn the ignition to ON then back to OFF.
d. Remove the key from the ignition.

5. Within 3 seconds, the power door locks should cycle (automatically)
indicating successful entry into programming mode. Return to step 1
if the locks do not cycle at this point.

6. Perform these steps within 40 seconds:

a. Press the LOCK and UNLOCK buttons on the transmitter
simultaneously for 1 second.

b. Immediately after letting go of the lock and unlock buttons,
press the lock button by itself and hold for 2 seconds.
Within 3 seconds, the door locks should cycle ( LOCK then
UNLOCK) once-- indicating successful programming. If
the door locks don't cycle, or cycle twice. Repeat steps
6a and 6b--this remote has not been accepted.

c. Repeat steps 6a and 6b for EACH transmitter that will
operate the vehicle. Including any old transmitters.

7. Close the driver door.
Good Luck

f
1. Start with the following conditions: you are in the vehicle

a. Key is out of the ignition
b. Drive door is open ( all other doors are closed)
c. Driver door is unlocked (other door locks don't matter)

2. Insert the key into the ignition (don't turn it) and pull it out.

3. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times. Use an even pace and try
to go relatively fast.

b. Close, then open the drivers door.

4. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times (same as before).
b. Turn the ignition to ON then back to OFF.
c. Turn the ignition to ON then back to OFF.
d. Remove the key from the ignition.

5. Within 3 seconds, the power door locks should cycle (automatically)
indicating successful entry into programming mode. Return to step 1
if the locks do not cycle at this point.

6. Perform these steps within 40 seconds:

a. Press the LOCK and UNLOCK buttons on the transmitter
simultaneously for 1 second.

b. Immediately after letting go of the lock and unlock buttons,
press the lock button by itself and hold for 2 seconds.
Within 3 seconds, the door locks should cycle ( LOCK then
UNLOCK) once-- indicating successful programming. If
the door locks don't cycle, or cycle twice. Repeat steps
6a and 6b--this remote has not been accepted.

c. Repeat steps 6a and 6b for EACH transmitter that will
operate the vehicle. Including any old transmitters.

7. Close the driver door.

Also can check this procedure: http://www.toyota-4runner.org/60925-post2.html

Hope this help.

v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} Normal 0 false false false MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} Here are the instructions for programming the 99-02 4Runner Keyless Entry factory remotes:

1. Start with the following conditions: you are in the vehicle

a. Key is out of the ignition
b. Drive door is open ( all other doors are closed)
c. Driver door

is unlocked (other door locks don't matter)

2. Insert the key into the ignition (don't turn it) and pull it out.

3. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times. Use an even pace and try
to go relatively fast.

b. Close, then open the drivers door.

4. Perform these steps within 40 seconds:

a. Cycle the power locks 5 times (same as before).
b. Turn the ignition to ON then back to OFF.
c. Turn the ignition to ON then back to OFF.
d. Remove the key from the ignition.

5. Within 3 seconds, the power door locks should cycle (automatically)
indicating successful entry into programming mode. Return to step 1
if the locks do not cycle at this point.

6. Perform these steps within 40 seconds:

a. Press the LOCK and UNLOCK buttons on the transmitter
simultaneously for 1 second.

b. Immediately after letting go of the lock and unlock buttons,
press the lock button by itself and hold for 2 seconds.
Within 3 seconds, the door locks should cycle ( LOCK then
UNLOCK) once-- indicating successful programming. If
the door locks don't cycle, or cycle twice. Repeat steps
6a and 6b--this remote has not been accepted.

c. Repeat steps 6a and 6b for EACH transmitter that will
operate the vehicle. Including any old transmitters.

7. Close the driver door.

Hope this helps you, it did me greatly-- Good luck,

1. Start with the following conditions: you are in the vehicle a. Key is out of the ignition
b. Drive door is open ( all other doors are closed)
c. Driver door is unlocked (other door locks don't matter)
2. Insert the key into the ignition (don't turn it) and pull it out.
3. Perform these steps within 40 seconds: a. Cycle the power locks 5 times. Use an even pace and try
to go relatively fast. b. Close, then open the drivers door.
4. Perform these steps within 40 seconds: a. Cycle the power locks 5 times (same as before).
b. Turn the ignition to ON then back to OFF.
c. Turn the ignition to ON then back to OFF.
d. Remove the key from the ignition.
5. Within 3 seconds, the power door locks should cycle (automatically)
indicating successful entry into programming mode. Return to step 1
if the locks do not cycle at this point.
6. Perform these steps within 40 seconds: a. Press the LOCK and UNLOCK buttons on the transmitter
simultaneously for 1 second. b. Immediately after letting go of the lock and unlock buttons,
press the lock button by itself and hold for 2 seconds.
Within 3 seconds, the door locks should cycle ( LOCK then
UNLOCK) once-- indicating successful programming. If
the door locks don't cycle, or cycle twice. Repeat steps
6a and 6b--this remote has not been accepted. c. Repeat steps 6a and 6b for EACH transmitter that will
operate the vehicle. Including any old transmitters.
7. Close the driver door.
Good luck and hope this helps.

this is form the owners manual, page 19:

The Automatic Door Locks can be enabled or disabled by
performing the following procedure:

1. Close all doors and place the key in the ignition
switch.

2. Cycle the ignition switch ON/OFF four times ending
in the OFF position. (do not start the engine)

3. Within 10 seconds of the final cycle, press the interior
driver’s door lock switch to the LOCK position.

4. A single chime will sound to signify that you have
successfully completed the programming.

You can turn the feature back on by repeating the above
mentioned procedure or by performing the procedure in
the Electronic Vehicle Information Center (EVIC), Customer
Programmable Features section on vehicles so
equipped.

If the key is not coming out of the switch, it may be off, but you haven't turned it far enough back that final click to remove the key. Some have a button you have to depress to get the key switch to turn back that final click. That's it.

Yes, there is a way to reprogram your car to lock the doors when the gear selector is put into Drive.
Follow this site for a complete step by step re-program of the door locks:
http://www.nialtima.com/automatic_door_locks-113.html