If it boots into WB from a cold boot, but not a warm boot - I cannot see how that could be a hardware failure.
As Thomas asked, you're sure you didn't leave a FD - or another bootable media with a priority higher than the HDD in its drive?
Other than that, all I can think of is that you somehow accidentally re-mapped the key sequence ctrl/Amiga/Amiga. A good start might be to temporarily restore the changes in your startup-sequence by commenting out the newly added lines, and take it from there.
Come to think of it, I can think of one hardware failure - and that would in this case be the keyboard.
