I thought I read something in my manual that the bike would start and shut down after a few seconds if the security was armed? Guess i better re-read some of that stuff. Never tried it myself, it was just a quick thought on the problem.
Been awhile since I set off my security, but I seem to remember it won't even crank if activated... just flashing lights and that obnoxious, optional siren on my '03...
Of course, if the security module is malfunctioning, anything is possible...