Are you 100% sure the immobilser has not been triggered into shutting things down?
When you put power direct to the starter motor and it cranks over does it start the motor then die a second or two later or does the motor not fire up at all when it is cranked over?
This may help confirm whether it could be the factory immobiliser. I have a 2000 Defender with the same key system (no fob) and had big problems with my immobiliser shutting down my ECU. 
With power direct to the starter motor, it would crank over and fire but died a second or two later.
If yours cranks and does not fire at all, maybe the problem lies elsewhere.
People suggested I try disconnecting the battery leads and holding them together for 30 seconds as this can 'clear' an ECU sometimes.
Also, low battery voltage can cause issues but it seems you've checked this already.
This advice from AULRO member Xtreme may be useful if the ECU settings have gone wrong for some reason: 
http://www.aulro.com/afvb/electronic...n-news-27.html (especially posts 255 to 260 and 267) He lists the correct Australian settings for the Td5 Defender, especially the one that enables/disables the Immobilizer.
Good luck.
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