The only time the immobilizer indicator should flash rapidly is when the system is in key re-registering mode. It could be the key(s) have become de-registered and/or the ECU has got stuck in key registering mode; in this mode the bike won't run. Try disconnecting the battery for an hour and see what happens when it is reconnected.

Here's something else worth a try and it won't cost you a penny:

Re-register both black keys with the ECU using the red key and see if that makes a difference. It is fairly simple to do provided you have the instructions in the service manual to hand.

If you haven't got access to the service manual, then get back to me and I'll find you the instructions, or alternatively join the 'XT660 Supporters Scheme' and get your manuals downloaded for 10GBP (see my signature for details).

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