I had this. Mine was a problem with the wiring in the fuse box. Basically to get the headlights working as the realy was shagged, some previous owner had bridged some fuses between eachother in the fuse box, this in turn was fucking up the immobiliser on my toad alarm.

I removed said wires and replaced the relay and I never got the problem after that.

My trick at the time was to start the car with the door open (something was really screwing with the alarm) and it would go ok. Also made the clock reset every time I opened the door!

Check there arent any fuses bridged!

Lee