@Kay
Would it be possible to have anything to do with the CDRom ddrive? Seems I recall something about the Amiga taking a certain amount of time before doing anything, waiting for some kind of signal from the CDRom. Just grabbing at straws, I'm not real techie material, but I seem to remember reading something about that. My A2000 used to take forever to boot, leaving a cd in the drive seemed to help.