Well, I also have an towerised A4000 with a WarpEngine 040 board, and I have the same problems... My tower is a Micronik 4000 ISA tower though (find more info on
www.amiga-hardware.com).
If I take out all kind of expansions out of the computer, so all that's is left is the cpu card, keyboard and the floppy, then the computer won't boot. To get it to boot I have to do the following...
1. Turn off the computer and then insert the floppy power cable the other way around and then power up.
2. The diskdrive LED is turned on all the time, because the cable has been inserted incorrectly. I then turn off the computer again.
3. I reassemble the diskdrive cable correctly once again, and when I power up the computer the purple screen usually pops up.
I have no clue what causes this, and I don't spend much time on solving this problem becuase of all the other computers that also take my time :-) But in the near future I will sit down and trace this ####ing bug. Something tells me that it's the floppy drive that's the problem though.
Please keep me informed if you get any progress. I will do that to of course.