Ok so when I put my GVP Trex II into my A4000D and swap the jumpers to Int on the MB my CF card stops being seen. I have tried several IDE CF adapters and the same thing happens on all of them with the 3040 I see it and with the Trex II I do not.
My System:
3.1 Roms
ZorRam 256
Cybervision 64/3d
8GB CF w/ Amiga OS 3.9 + BB1-3 installed