I got a WarpEngine with BB2 installed by I skip the exec library update which is slower and reported as buggy sometimes or certain situations. I've planned to give it a try on Piru's excellent exec.library replacement but till today I never bothered...
Anway, as someone said above if it was botting and the hardware config is the same it should be software. But from my experience with the A4000D a lot of stuff can have bad contacts. Sometimes I just have to push the CPU card a bit further after I moved the machine around, to make it work again.
The termination on the WarpEngine is also a pain. Have you changed any external device ? My chain is terminated by the external CDRom, I have to keep it on otherwise it won't boot. I tried once to get an external terminator (can't remember which) and it didn't work at all! And this was a terminator fot SCSI2.
