Remote control won't lock/unlock doors, but will open the trunk. What;s wrong?

Jeep 1990 and later Remote keyless entry programing

Put the key in the ignition with all doors and trunk closed

Open the driver's door on the automobile and leave the door open.

4 Move the switch on the door to the lock position while the door is open.

5 Switch the key in the ignition two clicks to the right to the "On" position. do not start

6 Press the lock button on your keyless remote for your Jeep and hold the button for 5 seconds. Release the button and remove the key from the ignition to complete the programming.

Read more : http://www.ehow.com/how_5019251_program-keyless-entry-jeep.html

Yes - Sometimes when the battery is replaced the key program can be corrupted. It would be a starting point to have the key reprogrammed just to eliminate it as a source of trouble.

Do any of the other buttons on the remote work, like the horn or trunk-open buttons? If they do, then you might have a blown fuse or relay switch for the specific problem. On my Grand Am, there are relays for "Door Lock", "Door Unlock" and "Driver Door Unlock".

When you press the trunk open button, do you hear any "release" noise come from the trunk area? The issue may be a bad battery in the key fob OR there could be an issue with the transmitter located inside the vehicle. Do the doors lock and unlock properly? is the vehicle equipped with security or immobilizer? please advise

this is a problem that can appear after your car battery died, cause the car didn't reset propely, so taking the battery out and putting it back in or letting your car die again would do the trick. I tried a lot of reprogramming procedured for my remote key, none of them worked, what did the trick though was simply unlocking the doors via the all door unlock button on the passenger side door, so simple.

Programming
When
Key added or replaced. System malfunction.
How
Driver's door open and key removed from ignition switch. Insert key into ignition switch, then remove it. Within 5 seconds: Insert key into ignition switch, then remove it. Within 40 seconds: Close and open driver's door twice. Insert key into ignition switch, then remove it. Within 40 seconds: Close and open driver's door twice. Insert key into ignition switch. Close driver's door. Switch ignition ON and OFF once to program a new key code whilst retaining the original codes or twice to program a new key code whilst erasing the original codes. Remove key. System should now lock and unlock vehicle, once or twice depending which mode has been selected. Carry out the following button procedure within 40 seconds: Press key lock or unlock button once. Within 3 seconds: Press same key lock or unlock button once. System should now lock and unlock vehicle.
NOTE: If system locks and unlocks vehicle twice, programming procedure has not been completed. Repeat button procedure.
If required repeat button procedure to program remaining keys.
NOTE: To exit programming mode: Open driver's door. NOTE: A maximum of 4 keys can be programmed

This will work providing printed circuit is not damaged in remote

You lost your program of the key module follow these instructions.

To Program a Remote for a VW
Put your good key in the ignition and turn to "ON", do not start the engine. Make sure all the remotes you want to use are present because they have to be programmed at the same time.
- Close the door and insert key #2 into the driver's side lock. Lock the door.
-Within 5 seconds of locking the door, press unlock 2 times on the new remote, key #2.
-(if this is remote #3, press unlock 3 times. if this is remote #4, press unlock 4 times).
-If there's a chirp or beep do not press it again. This means that the car has recognized the new keyless entry remote.
- Repeat with other remote or unlock the car and turn off - done.

It is entirely possible that the unlock button on the remote is worn such that it is not making contact. I've seen this happen many times, as the unlock button is pressed so much more than lock. You might try to reprogram the remote first before you look into getting a new remote. The procedure goes like this. Close and lock all doors Key in and out of the ignition 6 times, hazard lights should flash twice Turn key into accessory or on position Unlock and lock doors with drivers switch Press lock or unlock on remote Hazards should flash again to verify recognition turn key off  manually unlock door and then open and shut it.  you should then be able to test remote. 
The key to the procedure is doing step two quickly Hope this helps, if not you may need another remote or see dealer.

just found out it is the left front door latch assembly that failed on my car...so there is nothing wrong with the remote transmitter....dealer says $385.00..not happy but thats the answer i got

is the battery installed in the right orientation?