I know you've programmed the key to work remotely, but I have a how to guide to programme to the immobilser that you could try.
MK1 st
Programming
When
System malfunction: LED illuminates for 1 minute, then flashes at irregular intervals.
Key(s) added or replaced.
NOTE: Replacement keys MUST have blue mark. Keys with red mark are NOT compatible with this system.
How
NOTE: Programming method using vehicle keys can be deactivated using diagnostic equipment.
Obtain 2 programmed keys (A and B).
Insert key A into ignition switch.
Turn ignition switch to position II. Wait 1 second.
Switch ignition OFF. Remove key A.
Insert key B into ignition switch within 5 seconds.
Turn ignition switch to position II. Wait 1 second.
Switch ignition OFF. Remove key B.
Within 10 seconds:
Insert key to be programmed into ignition switch.
Turn ignition switch to position II. Wait 4 seconds.
Switch ignition OFF. Wait 5 seconds.
Start engine.
If engine does not start and clock LED flashes:
Switch ignition ON. Wait at least 20 seconds.
Switch ignition OFF. Repeat programming procedure.
Repeat above procedure to program remaining keys.
Keys can also be programmed using diagnostic equipment.
NOTE: A maximum of 8 keys can be programmed, including a maximum of 4 with remote control.
NOTE: If the system is in spare key programming 'disabled' mode, the above procedure will not work. Diagnostic
equipment will be required to change to spare key programming 'enabled' mode.