1999 SUBARU IMPREZA NOT STARTING, FLASHING FRONT AND TAIL LIGHTS, DOORS UNLOCKING AND LOCKING, WEIRD CLICKING FROM KEYLESS ENTRY BLACK BOX, BATTERIES DRAINED?

The RKE is controlled by the SJB - smart junction box ! Fords BCM - body control module .
Principles of Operation
Power Locks
The SJB controls the power lock/unlock feature of all of the vehicle doors, including the liftgate, to lock or unlock based on the input received from the door lock control switch, the keyless entry keypad or the remote keyless entry (RKE) transmitter. Power locking and unlocking of the doors function independently of the key position, vehicle speed or transmission position. The smart junction box (SJB) activates internal relays to supply the correct voltage and grounds for the door lock actuators.

Your best bet would be to take to ford dealer or some other qualified repair shop .
Remote Keyless Entry (RKE) Transmitter Lock/Unlock Control - Unlock
The RKE transmitter feature provides lock/unlock functions independently of key position, vehicle speed, or transmission position. The RKE transmitter feature provides a 2-step process for unlocking the doors. Upon receipt of the first request for unlocking the doors, the RKE control feature requests the SJB to unlock the driver door only. If another unlock request is received within 3 seconds of the first, the RKE transmitter feature requests the SJB to unlock all the doors. This feature can be changed to global unlock, so that all the doors unlock on the first press of the unlock button. To toggle between the 2-step unlock and the global unlock press the lock and the unlock button on the RKE transmitter at the same time and hold the buttons for 4 seconds. The turn signal lamps flash to confirm that the feature has been toggled.
Remote Keyless Entry (RKE) Transmitter Lock/Unlock Control - Lock
The RKE transmitter feature requests that all the doors be locked when the lock button is pressed. On any press of the lock button with all doors closed, the SJB provides 1 flash of the parking lamps. If any door is ajar, no flash occurs. As soon as the last door is closed, the SJB provides the flash of the parking lamps. If 2 presses of the lock button are received within 3 seconds, the horn chirps once, and the parking lamps flash twice to indicate that all the doors are closed and locked. If any door is ajar when the second lock request is received within 3 seconds of the first, the RKE transmitter feature requests the SJB chirp the horn twice without flashing the parking lamps to indicate it locked all the doors but 1 or more doors are ajar. When the key is in the ON or START position, the parking lamp flashes and horn chirp confirmations do not occur.

All locks not working ?????

• The doors do not lock/unlock using the remote keyless entry (RKE) transmitter

• RKE transmitter battery
• RKE transmitter
• RKE transmitter programming
• Aftermarket system
• SJB

• Go To Pinpoint Test H .

The keyless entry system consists of the following components:

• driver door module (DDM)
• keyless entry transmitter
• keyless entry keypad

The driver door module (DDM) receives inputs from the digital transmission range (TR) sensor, ignition switch, brake switch, window/door lock switches, lighting control module (LCM), keyless entry keypad switch and remote transmitter. The DDM outputs consists of keyless entry keypad switch illumination, power door lock actuators, luggage compartment release solenoid, horn relay, and lighting control module (LCM).

• Battery junction box (BJB) fuses:
  • circuit breaker 7 (20A)
• Central junction box (CJB)
  • 4 (10A)
  • 6 (15A)
  • 8 (25A)
  • 13 (5A)
• Keyless entry keypad switch
• Power door lock actuator
• Luggage compartment release switch
• Luggage compartment release solenoid
• Connectors or connections
• Wiring harness
• If fuse's good have checked for DTC'S - diagnostic trouble codes .
• B1526 Keyless Entry Circuit Short to Ground DDM Go To Pinpoint Test E . B1553 Decklid Release Circuit Short to Battery DDM Go To Pinpoint Test B . B1751 Park/Neutral Switch Circuit Short to Battery DDM Go To Pinpoint Test K . B2425 Remote Keyless Entry Out of Synchronization DDM Go To Pinpoint Test L Need a professional grade scan tool to check fro these codes . Not a code reader for OBD2 codes .

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

• Remote transmitter not programmed.
• Remote transmitter.
• DDM.

• Go To Pinpoint Test F .

Did you program the new key fob ?

Remote Transmitter Programming NOTE: All remote transmitters are programmable and must be set at the same time.

1. Turn the key from OFF to RUN four times within three seconds, ending in RUN. The locks will then lock and unlock, confirming program mode has been entered.

1. Press any button on each remote transmitter to be programmed. The doors will lock and unlock to confirm that each remote transmitter has been programmed.

1. If additonal remote transmitters are to be programmed, repeat Step 3 within 7.5 seconds or steps 2 and 3 if more than 7.5 seconds have elapsed.

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

1. NOTE: Failure to wait at least 20 seconds will cause programming failures. Wait at least 20 seconds after turning the key to OFF or after the last remote transmitter has been programmed to activate a remote transmitter for testing or verification

Sounds like your cars battery is dead. Try charging it. Even if it starts after you charge it, it may need a new battery.

Keyless Entry
The keyless entry system consists of the following:

• smart entry control(SEC)/timer module
• keyless entry remote transmitters
• power door lock actuators
• body side door power door lock actuator
• liftgate actuator
• power door lock switches
• door ajar switches
• Principles of Operation
  All doors can be locked at once by turning the door key lock switch to the locked position. An individual door can be unlocked by moving the door key lock switch to the unlocked position and turning it again within five seconds; all the doors (including the liftgate) will unlock.
  The smart lock system is designed to keep the driver from locking his keys in the car. It will lock and then unlock all the doors if the smart entry control(SEC)/timer module detects the following conditions:
  
  • The ignition key still in the ignition.
  • A front door is open.
  • A door lock switch has been pushed to the lock position.
  The panic feature has a duration of 30 seconds from the last time the PANIC button is pressed. When locking the doors from the remote transmitter, the horn chirp/lamp flash feature can be disabled or enabled by holding the LOCK and UNLOCK buttons for two seconds. The hazards will flash three times to confirm that the feature has be enabled or disabled.

The control module probably see's an input that shouldn't be there . lock Switch , door ajar etc... Don't think it has anything to do with the remote . Some part stores have a tester to see if signal from the remote is working . Or the dealer ! Take it an see if your remote is sending a signal without you pressing any buttons .
If it is you need a new one .

TRY THIS REPROGRAMMING PROCEDURE. SWITCH THE IGNITION OFF TO ON 8 TIMES WITHIN 10 SECONDS. DOORS SHOULD LOCK THEN UNLOCK. PRESS ANY BUTTON ON THE FIRST REMOTE TRANSMITTER. DOORS SHOULD LOCK THEN UNLOCK. IF YOU HAVE ANOTHER CAR REMOTE REPROGRAM IT THE SAME WAY. WHEN DONE SWITCH IGNITION SWITCH OFF.

Battery Constant 12v+ Positive Wire (+): Black/Yellow
Battery Constant 12v+ Positive Wire Location: Ignition Switch Harness

Starter Positive Wire (+): Blue/Red
Starter Positive Wire Location: Ignition Switch Harness

Ignition Positive Wire (+): Red
Ignition Positive Wire Location: Ignition Switch Harness

Accessory Positive Wire (+): Red/Yellow
Accessory Positive Wire Location: Ignition Switch Harness

Parking Light Positive Wire (+): Red
Parking Light Positive Wire Location: Low In Drivers Kick Panel

Power Door Lock Negative Wire (-): Add Actuator. This vehicle uses a central door locking system. When connecting a keyless entry, you will need to add a door lock actuator and some units will also require (2) extra relays.
Power Door Lock Negative Wire Location: To Drivers Door Only

Power Door Unlock Negative Wire (-): Add Actuator. This vehicle uses a central door locking system. When connecting a keyless entry, you will need to add a door lock actuator and some units will also require (2) extra relays.
Power Door Unlock Negative Wire Location: To Drivers Door Only

Door Trigger Negative Wire (-): Red/White
Door Trigger Negative Wire Location: In Black Plug, Above Hood Release

Domelight Supervision Wire: Use Door Trigger, Requires Relay
Domelight Supervision Wire Location: N/A

Horn Negative Wire (-): Red/Green
Horn Negative Wire Location: At Steering Column Harness

Tachometer Wire Negative Wire (-): Black/Blue
Tachometer Wire Negative Wire Location: At ECM, Under Drivers Side Dash

Brake Light Positive Wire (+): White/Black
Brake Light Positive Wire Location: At Switch Above Brake Pedal

CODE ALARM SYSTEM

Used on:
Impreza 1996-2001
Legacy 1995-1999
Forester 1998-2000

Battery GP-23A

Lock: Left button will lock all doors. Double chirp indicates locked.
Unlock: Right button will unlock driver's door only. Hold unlock button app 6 seconds, it will unlock all doors including rear gate. Single chirp indicated unlock.
If the car chirps or lights flash 4x the alarm was triggered.
Panic. Press both buttons to activate emergency honk and flashing lights.
Valet mode: With optional alarm onlyPress the red alarm button on the left of the steering wheel. The light will quickly double flash. To re-set back to normal mode, press the red alarm light button again

Battery failed and lights flashing?
Parking lights will flash when the vehicle's battery is disconnected and reconnected.
To stop lights from flashing, either:
Press remote transmitter "UNLOCK" button once OR turn the ignition switch to the "ON" position and press programming button for one second (see below).
The vehicle interior (courtesy) light and door open warning light (DOOR AJAR indicator) will then illuminate for 60 seconds when the ignition is turned off, or until the doors are locked with the remote transmitter. Yes, the dashboard instrument panel lights will flash when the parking lights flash.

Programming or Overriding the Alarm when you have lost the remote
Open driver's door.
Turn ignition key to 'On'
Press and *hold programming button* in (see diagram, button under dashboard)
After 15 seconds the the door locks will cycle 3 times. Do not release Programming button.
Press lock (left) button the remotes to be programmed. The door locks will cycle one time. Exit programming mode by releasing Programming button under dashboard and turning key to off.

Code Alarm Programming Button is under dashboard on the kick panel by the driver's left knee, left of the steering column. If you can't find it, it might still be tucked up in the wiring harness higher up in that same general area. The botton is recessed in a plastic ring (see diagram).
This button must be pressed while programming remotes or if the battery was disconnected and the lights are flashing.

what do you mean keyless entry? don't you have a remote unlocker?

first unlock car manually with key remove driver side kick panel/lower A pillar trim connect locking registration wires together(two white connectors,black wire and black and blue wire)press and hold central locking switch on drivers door in the unlock position .interior lamp will flash and an acoustic sound will be heard. now get your key and press unlock and then lock the door should lock then unlock, job done ,i persume it was to program the fob to work the central locking u wanted

usually after opening the door you can deactivate the alarm by pushing th unlock button or simply insert keyy in ignition and turn it on.

The keyless entry is designed to work with the doors closed (closed - not locked). If the door ajar sensor thinks the door is open the keyless entry is disabled. When you manually lock the door it might tighten the door just enough to activate the keyless entry. I would try slamming all the doors closed and then see if the keyless entry works. If it still wont work have the wiring checked on the front door lock.