I've had a similar experience. I have an Amiga 500 (motherboard rev 6 with 1mb onboard ram modded to chipram and kickstart 2.04) and an ACA1230/42.
With the latest firmware choosing any maprom profile, it disables the 1230 fast ram and the Aux CF slot. If I go to the expert menu and enable "add other on-board ram" and "AUX CF slot" (F5 and F8) while keeping disabled the maprom function ("Map ROM: off" and "ROM: keep current") I can get the Aux CF slot working and all fast ram enabled successfully.
I haven't tried an older firmware yet. I've tried a Blizzard 1230 IV and it works flawlessly.