When using remote to unlock or lock doors the motor keeps going for a couple of seconds and when driving it will stop and start

keys into ignition turn to number 2. press fob. doors lock press again doors unlock. turn ignition back remove key. press fob lock doors wait 5 seconds press fob to open doors. then try ignition again. should work. if not then there is something like a chip missing from the key or the ring reader on the ignition is not working.

probably the FOB, just because other functions work does not mean that the lock/unlock will work. This is the most used function and the one that goes first.

Few Toyota models came equipped with remote door locks before 2008 - surprisingly!

Your car may not have the radio receiver to work with door locks. In that case, you need the radio and some wireing to pair with your remotes.

Try reporgraming it

1. Start with key out of ignition, drivers door is open all others closed and
drivers door is unlocked.
2. Insert key into the ignition (Do NOT Turn) and Pull key out.
3. Perform these steps within 40 seconds.
A. Using the power lock switch on the drivers door, perform 5 lock/unlock cycles
starting with lock. Use an even pace and try to go about one cycle per second.
(1Cycle = 1 lock and 1 unlock).
B. Close, then open drivers door.
4. Perform these steps within 40 seconds.
A. Using the power lock switch on the drivers door, perform 5 lock/unlock cycles
starting with lock. Use an even pace and try to go about one cycle per second.
(1Cycle = 1 lock and 1 unlock).
B. Insert the key in the ignition cylinder.
C. Turn the ignition to ON (Do NOT Start) then back to OFF.
D. Remove the key from the ignition.
5. Press any button on remote for a minimum of 1 second.
System should now lock and unlock doors once.

6. Close and open drivers door.
7. Press any button on remote for a minimum of 1 second. System should now lock and
unlock doors. Once to confirm programming, twice to indicate programming failed.
8. Repeat steps 5, 6 and 7 for additional remotes.

Watch these three videos ! Door Locks Go Crazy 1

Door Locks Go Crazy 2

Door Locks Go Crazy 3

The keyless entry system is controlled by the (GEM) - generic electronic module .
Keyless Entry The electronic door lock system has two main components:

• generic electronic module (GEM)(14B204)
• keyless entry remote transmitter (15K601)
• NOTE: Battery power and ground must be remove before disconnecting the GEM connectors to avoid setting false codes.
  Power Locks Operation The power locks feature allows the customer to lock and unlock the doors via momentary switches located on the driver and passenger door. When the GEM detects a momentary press of the driver or passenger lock button, the GEM will supply power to the driver or passenger lock actuators for approximately 250 ms from relays internal to the GEM. When the GEM detects a momentary press of the driver or passenger unlock button, the GEM will supply power to the driver or passenger unlock actuators for approximately 250 ms from relays internal to the GEM.
  Remote Keyless Entry Door Locks Operation The remote entry feature allows the customer to unlock the driver door, unlock all doors, and lock all doors using a valid remote transmitter as long as the ignition switch is not in RUN or START. The driver door is unlocked whenever the GEM detects a valid remote transmitter unlock transmission. All the doors are unlocked when the GEM detects a second valid remote transmitter unlock transmission within three seconds of the first transmission. All the doors are locked when the GEM detects a valid remote transmitter lock transmission. If the GEM detects a second valid remote transmitter lock transmission within three seconds of the first transmission, the doors will lock again, the horn will sound for 20 ms and the parking lamps will flash for 200 ms to indicate the doors are locked. If the GEM detects the driver or passenger door is ajar during the second lock transmission, the doors are locked again and the horn is sounded twice. If the GEM detects a valid remote transmitter lock transmission within three seconds of detecting a valid remote transmitter unlock transmission, the GEM will lock all the doors
• • The doors do not lock/unlock using the remote transmitter
  • Ignition switch.
  • GEM.
  • Remote transmitter.
  • Remote transmitter batteries.
  • GO to Pinpoint Test C .
  You followed the program instructions to the letter ? Programming -Keyless Entry Remote Transmitter NOTE: All keyless entry remote transmitters (15K601) must be programmed at the same time.
  NOTE: All previous transmitter identification codes (TIC's) will be erased when programming mode is entered.
  NOTE: To program (or reprogram) the keyless entry remote transmitters into the generic electronic module (GEM)(14B204), perform the following steps.
  
  1. Turn the ignition from OFF to RUN eight times within 10 seconds, ending in RUN. If the GEM has successfully entered program mode, it will lock and unlock all the doors.
  1. NOTE: The first TIC must be entered within 7.5 seconds of entering the program mode and additional TICs must be entered within 7.5 seconds of the first TIC. The programming mode is exited whenever the timing constraints are not met.
     Press any button on a keyless entry remote transmitter, and the doors will lock and then unlock to confirm that each keyless entry remote transmitter has been programmed.
  1. If the door locks do not respond for any keyless entry remote transmitter, wait for several seconds and press the button again.
  1. Turn the ignition switch to the OFF position, or wait up to five minutes after step 1, to exit program mode. If a keyless entry remote transmitter has been programmed (or reprogrammed), the GEM will lock and unlock all the doors one last time.
  1. Take an have the vehicle checked for DTC'S

B1396 Power Door Lock Circuit Short to Battery GEM GO to Pinpoint Test B . B1397 Power Door Unlock Circuit Short to Battery GEM

Unhook negative battery post for about a minute then reconnect. never hurts to change remote batterys, make sure you get all the water out of doors drill a whole in bottom of door if you have to

Programming
When
Key batteries completely discharged. Key batteries not replaced within 60 seconds. Key added or replaced. DO NOT press remote control buttons during battery replacement.
How
Unlock vehicle. Enter vehicle. Close driver's door. Switch ignition ON and OFF. Remove ignition key. Press and hold unlock button Fig. 1 [1]. Press lock button Fig. 1 [2] briefly 3 times within 10 seconds keeping unlock button [1] depressed. Release unlock button Fig. 1 [1]. Some models: LED Fig. 1 [3] flashes slowly for 10 seconds. Some models: Central locking system locks and unlocks rapidly to indicate correct programming. Some models: Repeat above procedure if central locking system does not work and LED does not flash or LED flashes continuously

To change batteries remove panel back of key then screws on plastic bar
Batteries are available from your local motor factor shop
You might not need new batteries try re programing as described above

1. Start with key out of the ignition, drivers door is open all others closed and
drivers door is unlocked.
2. Insert key into ignition (Do not turn) and pull it out.
3. Perform these steps within 40 seconds.
A. Using the power door lock switch on drivers door perform 5 lock/unlock cycles starting
with lock. Use an even pace and try to go about one cycle per second.
(1 cycle = 1 lock and 1 unlock.)
B. Close, then open drivers door.
4. Perform these steps within 40 seconds.
A. Using the power door lock switch on drivers door perform 5 lock/unlock cycles starting
with lock. Use an even pace and try to go about one cycle per second.
(1 cycle = 1 lock and 1 unlock.)
B. Insert the key in the ignition cylinder.
C. Turn the ignition to ON (Do NOT Start) then back to OFF.
D. Turn the ignition to ON (Do NOT Start) then back to OFF.
E. 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 remote 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 once indicating successful programming. If the door locks don't cycle or
cycle twice, repeat steps A and B, your remote has not been accepted.
C. Repeat steps A and B in step 6 for each new transmitter.
7. Close drivers door.

try this:

1. Start with key out of ignition, drivers door is open all others closed and
drivers door is unlocked.
2. Insert key into the ignition (DO NOT Turn) and Pull key out.
3. Perform these steps within 40 seconds.
A. Using the power lock switch on the drivers door, perform 5 lock/unlock cycles
starting with lock. Use an even pace and try to go about one cycle per second.
(1Cycle = 1 lock and 1 unlock).
B. Close, then open drivers door.
4. Perform these steps within 40 seconds.
A. Using the power lock switch on the drivers door, perform 5 lock/unlock cycles
starting with lock. Use an even pace and try to go about one cycle per second.
(1Cycle = 1 lock and 1 unlock).
B. Insert the key in the ignition cylinder.
C. Turn the ignition to ON (Do NOT Start) then back to OFF.
D. Remove the key from the ignition.
5. Press any button on remote for a minimum of 1 second.
System should now lock and unlock doors once.

6. Close and open drivers door.
7. Press any button on remote for a minimum of 1 second. System should now lock and
unlock doors. Once to confirm programming, twice to indicate programming failed.
8. Repeat steps 5, 6 and 7 for additional remotes.