My keyless entry remote opens trunk but doesnt lock and unlock doors and start the engine

NO FOBS DETECTED
Refer to Keyless Entry System Description and Operation

Keyless Entry System Description and Operation - Passive
Passive keyless entry allows entry to a locked vehicle without pressing any buttons on the keyless entry transmitter. You must only have the transmitter with you. This passive system is also part of the vehicle starting system. It allows you to start and run the vehicle having only the transmitter as your key. The passive entry and starting system use low frequency antennas in 4 different areas on the vehicle to determine the location of the transmitter. When passively opening a locked door or the rear compartment lid, you must have a programmed transmitter with you in your pocket, purse, or briefcase. As a customer opens the door handle or presses rear compartment touch pad, the low frequency antenna sends out a challenge to the keyless entry transmitter. The transmitter must be in a one meter range of the door or rear compartment lid in order to receive the challenge. If the challenge is met, the transmitter will respond, allowing the door to be unlocked and opened. Passive entry allows you to operate the following features:
• Passive door unlock/unlatch
• Passive rear compartment lid release
• Illuminated entry lamps
• Vehicle starting
The keyless entry system has the following components:
• Keyless entry transmitters
• LH and RH door antennas (part of the door handle assembly)
• Rear compartment antenna
• Console passive antenna
• Console active antenna
• Instrument Panel Module (IPM)
• Rear Integration Module (RIM)
• Remote Control Door Lock Receiver (RCDLR)
• External RF Antenna (includes coax from RCDLR to back glass)

Remote Control Door Lock Receiver (RCDLR)
The RCDLR is a multi-function module which controls all the vehicles antennas for passive keyless entry functions. The RCDLR also acts as the receiver for active keyless entry and tire pressure monitoring (TPM) functions, as well as controlling all immobilizer functions.
The RCDLR's RF antenna is located in the back glass, and there is a coax cable connecting the glass antenna to the module located in the trunk.

Your best bet , take it to a qualified repair shop that has the factory Tech 2 scan tool or someother professional type scanner that can read • Rear Integration Module (RIM) DTC'S - diagnostic trouble codes .

Probably the battery in the remote. Would check that first. Let me know if that works before getting deeper into it.

Have you tried to change the batteries again?

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

Programming Electronic Door Lock Control System NOTE: The electronic door lock control processor (14B001) erases all previous keyless entry remote transmitter (15K601) from memory when the keyless entry remote transmitters are programmed or reprogrammed. The electronic door lock control processor can store up to four keyless entry remote transmitters in memory.

• To program (or reprogram) keyless entry remote transmitter into the electronic door lock control processor, perform the following steps:

1. Turn ignition switch to the RUN position and momentarily short the two terminals of the program connector taped to the wire assembly and located behind the glove compartment. All doors should lock and then unlock. Remove shorting pin.
   

1. Press any button on keyless entry remote transmitter. All doors should lock and then unlock to verify the keyless entry remote transmitter has been programmed. If door locks do not respond, press button again (up to three times maximum with the same keyless entry remote transmitter).
   

1. Repeat the above step to program additional keyless entry remote transmitters into the electronic door lock control processor (up to four keyless entry remote transmitters maximum).
   

1. Turn ignition switch OFF. All doors should lock and then unlock.
   

1. Check operation.
   

security module in the trunk ???? There is no security module in the trunk . What light's come on by them self ? Park lamps , headlamps , brake lamps ,turn signals etc.... The module for anti-theft is under the right hand side of the dash . The remote keyless entry module is located in the trunk. Is this the part you hear clicking in ?
Door Lock Control Processor, Electronic NOTE: The electronic door lock control system will not function when the ignition switch is in the RUN or ACC position.
The electronic door lock control processor:

• is located on the LH side of the luggage compartment.
• contains a radio receiver that receives a signal from the keyless entry remote transmitter (15K601) through electronic door lock control processor antenna, and sends the appropriate command to the power door locks, the horn relay, the indicator flasher, or the anti-theft warning system.
• is equipped with a battery backup which holds the programmed code in memory in the event the vehicle battery is disconnected.
• • Doors Do Not Lock or Unlock Using Keyless Entry Remote Transmitter
  • Circuit.
  • Electronic door lock control processor.
  • Keyless entry remote transmitter.
  • GO to Pinpoint Test B .

Open the remotes up...Are the boards the same...?

does trunk button work? panic button?
here's 2003 info:

• The doors do not lock/unlock using the remote transmitter

• Remote transmitter.
• Driver door module (DDM).

• Go To Pinpoint Test G .

SECTION 501-14: Handles, Locks, Latches and Entry Systems 2003 Town Car Workshop Manual
GENERAL PROCEDURES Remote Transmitter Programming

1. Cycle the ignition from OFF to RUN four times within three seconds. The locks will then lock and unlock, confirming that the program mode has been entered.

1. NOTE: When the first keyless entry remote transmitter is programmed, all other keyless entry remote transmitters are erased.
   Press any button on the transmitter to be programmed.

1. If additional keyless entry remote transmitters are to be programmed, repeat Step 2 within 7.5 seconds.

1. To exit program mode, turn the ignition to START or wait 7.5 seconds.

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There is 3 relays in one of the fuse panels that are labeled doorlocks one of them is probably bad. Push the door lock button and find the one that is clicking this is the one that is back. This should fix your problem

" turn the key on engine off 8 times. the doors will lock and unlock. push one of the buttons on the key fob and the doors will lock and unlock. do this for each remote that you have. when you are done turn the key off. the door locks will lock and unlock. the remote fob should work after this."
From My SecuriLock..