Hazard lights don't flash when using the keyless entry locking and unlocking the doors flashers and hazard lights work when using them on the hazard switch and indicaiter arm and everything on the locking system works I have checked the fuses all windows and doors are closed checked the door light switches have checked the fuses

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 .

may be factory service and repair manual can help you to fix the problem so i suggest you a link which will help you to fix the problem with manual http://toolsnyou.com/

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 .

When you are using the keyless entry you are flashing the turn signals... which are also the brake lamp filiment.
The park lamps on that side of the car simply dont work.
There is probably an open somewhere in the wire to that lamp. The lamps are fed through the wiring harness on the drivers side. Your break in the line is somewhere between the left and right in the rear. You can try to find it or run a jumper from left to right under the rug and save some pain. Your call.

The horn chirp can be disable by pressing the lock and unlock buttons simultaneously until the hazard lights flash, and no enable press the lock and unlock until the horn chirp.
To reprogram (enter new ID) key fob (keyless remote controller) follow the steps.
1. Close all doors and lock all doors
2. Insert and remove the key from the ignition key cylinder more than six times within 10 seconds. (The hazard warning lamp will then flash.) NOTE: Key should be withdrawn from ignition key cylinder completely each time.
NOTE: Do not rush the insertion/removal key cycling process. The side marker/tail/license lamps and interior illumination will flash twice when this step is accurately completed.
3. Insert key on ignition key cylinder and turn ignition key switch to "AAC" position At this time, the new ID code is entered and original (previous) ID codes are erase.
4. Press any button on the new remote controller once. (The hazard warning lamp will then flash)
NOTE: Do not press the button more than one time in the above step. If the button is pressed more than one time, the programming procedure will not be successful. The side marker/tail/license lamps and interior illumination will flash twice when this step is accurately completed and programming is successful.
If there is only one remote controller skip step 5.
5. Additional ID code entry Release the door lock, then lock again with door lock/unlock switch (In power window main switch)
6. Remove key from ignition
7. Unlock driver side door, open driver side door and then close the door. (END)

if its early 05 round heart shaped remote it needs programming into system at dealer with Tech2
later 05 to 07 had square (rectangle) shaped remote
1.2 ID Code Additional Registration
Note: This procedure will add additional remotes to the Keyless Entry Control Units memory. A total of 4 remote transmitters may be programmed into the Keyless Entry Control Units memory. When a total of registered and newly registered remotes exceed 4, the oldest one shall be erased.
Step Action
1 Note: Make sure that all the doors are closed and unlocked. Insert the ignition key into the ignition switch.
Open the driver's side door.
2 Turn the Ignition key to the “ON” position and then to the “LOCK” position three times
(The key should remain in the “LOCK” position)
Note: This step must be carried out within five seconds.
3 “CLOSE” and “OPEN” the driver’s doors once (Leaving the driver’s door in the “OPEN” position)
Note: This step must be carried out within five seconds after step 2 is completed.
4 Wait for 8 seconds (This wait time is critical)
5 Turn the Ignition key “ON” and then to the “LOCK” position once and turn key to the “ON” position (The key should remain in the “ON” position)
OR on/lock once
Note: This step must be carried out eight seconds after step 3 is completed.
6 “CLOSE” the driver’s door
The HAZARD lights should flash 3 times (This acknowledges the Keyless Entry Control Unit has entered programming mode)
7 Operate the lock or unlock button of the transmitters to be programmed; a flash of the HAZARD lights indicates the remote has been successfully programmed into the control unit
8 The HAZARD lights will flash approx 4 seconds after pressing the remote button to indicate the Keyless Entry Control Unit has exited programming mode.

If it is a 2003 model year vehicle follow this procedure. If it doesn't work, you may have the wrong fob which happens all the time.

Sit in vehicle and close all doors.
COMPLETELY insert and remove ignition key more than six times within 10 seconds.
Hazard lights should flash twice.
Turn ignition to ACC position
Press and hold any button on the new key fob hazard lights will flash twice
For a second key fob using the master lock switch, lock and unlock the doors then hold down any button on the second remote until the hazard lamps flash twice.
Then you are done open the door to exit the programming mode.
If the lamps didn't flash when holding down the key fob make sure you have the right key fob, they are different for each car.

The title of you problem mentions the horn but the actual problem mentions the flashers? Which is it? You can turn the 'horn beep' feature on and off by simultaneously holding the lock and unlock buttons down on the remote for about 3 seconds or more. When the horn feature is turned on you will hear the horn, and when it turns off you will only see the lights flash.

Close all vehicle doors, LOCK doors using drivers side switch.

Insert key all the way into the ignition, (do not turn) remove key.

Repeat this step 5 times. (6 total)

Hazards should flash to indicate program mode.

Press any button on transmitter to be programmed, hazards should flash to indicate successfull program.

*For additional remotes, cycle drivers door lock UNLOCK, LOCK, press any button on remote, hazards should flash. Repeat step as necessary.

Ignition ON, (engine off) ignition OFF, UNLOCK using drivers side switch, test remotes.

Source

You need to program the remote. Get in to the car and LOCK all doors with the switch on drivers side door. Take the key and insert it into the ignition cylinder in and out 6-10 times, until the flashers/hazards flash on your dash board. Or just keep putting the key in and out (nice and easy now, not fast) until you see the lights on dash flash. After the lights flash, turn the key into ACC mode to make the whole dash light up.(do not start car) .With the key in ACC position, hit any button on remote, that will make the hazards flash again. Turn key off and unlock door with switch again. Open door.DONE.
Good luck.