When you had it working with 3.1 on the CF, did you have IDEFix installed and running ?
I've read a couple of people on here saying IDEFix is incompatible with CF cards,dunno how true it is.
Edit.. I *really* should read more carefully!!
Since it worked with 3.1 and IDEFix, then the likely culprit is somehow the startup sequence is still telling Setpatch to load the new scsi.device
Just to make sure, edit s:startup-sequence and make sure any mention of Setpatch says C:SetPatch QUIET SKIPROMUPDATES "scsi.device"
