Hi,
as already said, I would also try to use the original Amiga keyboard. Which adapter do you use to attach the PC-keyboard to your Amiga? Does it require any software to run? Maybe here is your problem. Or any other program you start during booting is unable to run correct on an 68040 and produces the trouble.
Go through the early boot menu and try to boot without startup-sequence.
I hope you have installed Kickstart 3.1? In any other case you get into trouble with an A3640.
Noster