1999 Ford Mondeo remote locking not working

Could try this ,


Reprogram a Remote Key after changing the Battery
Difficulty:


Required Tools: None
Time Required: 5 mins

Turn the key to so the dash lights come on (last stage before starting the car) and off again 5 times.
Get out of the car and press the button to lock it. The red light in the clock should come on.
Get back in, turn the key to the last position again and count to 10 slowly. Then turn ignition off,
Get out of the car again and now it should lock properly.
This info shamelessly stolen from a post on the Ford Mondeo Org Forums by MobyDick, ta!

Here is another set of instructions that may work, as there seems to be several different mechanisms depending on your model

Put the remote key in the ignition and switch on and wait for the led to go out.
Then switch from positions 3 to 2, 3 to 2, 3 to 2, 3 to 2. This must be done quite fast you may need to experiment at the speed and is done 4 times.
At this stage the alarm LED will Stay on. As soon as the Led is on press and hold down the UNLOCK button on the remote for about 4 or 5 seconds.
The LED will then flash 4 times to say the code is accepted.
Remove key. wait a few seconds and test.
Here is a set of instructions from the Ford TSI CD

Unlock the vehicle.
Turn the ignition key from position '0' to position 'I' (accessory position), then wait in position 'I' until the LED in the clock lights up after approximately 10 seconds.
Turn the ignition key to position '0' again while the LED in the clock is lit. Remove the key, the LED remains lit.
Hold the remote control key in front of the external receiver (in external door handle) of one of the front doors and press, and hold down, one of the two transmitting buttons. After approximately one second the LED on the key will flash once.
Continue holding down the button on the key after the LED on the key flashes once and with the other hand press the other button three times. Then release both the buttons.

NOTE:
Hold the key in front of the receiver until the LEDs have flashed five times.


The LED on the key and the LED in the clock should flash five times.
To programme other remote control keys, repeat sub-operations 11 to 13 before the LED in the clock goes out (after approximately 20 seconds).
After programming the remote control key, briefly switch the ignition on and off. The LED in the clock should go out.
From Franky De Caluwe

If you have a Mondeo 2001 (mk3) with a remote control for the central locking you can change the strategy of opening the doors.
The normal mode is: push on the unlock-button once and all doors open.
Second mode is: push on the unlock-button once and only the drivers door will unlock. Push a second time on the unlock-button and the other doors will open. Push on the lock button and all the doors will be locked.


You can switch between this two strategies: hold the lock and unlock button on the remote control at the same time and wait until the turning lights on the car go on and off.
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Dismantle key * remove battery (CR2032 type as used in Computer Motherboards and in Nationwide Bank Card Reader) * spray battery contacts with 'Contact Cleaner (available online or PCWorld or Maplins) * replace battery * try it. It works with me every time, but is not long-lasting solution and this fix will need repeating.