I would suggest double checking FastATA controller. See if it sits inside the rom sockets securely (god I hate how they designed this, with the cable ties holding it through motherboard holes designed for 2.5" hd cradle).
I've had lots of trouble in the past with FastATA and BPPC cards due to weak contacts with the FastATA controller and rom sockets, as the controller really, and I mean really needs to be tightened well with cable ties unless you want it to pop out. I would suggest checking if FastATA is seated well.
ATA3Prefs utility almost always declares that a BPPC card is defective. I also suspect that this is related to poorly seated FastATA controller in the rom sockets.
Try removing FastATA altogether and use the native IDE controller, just for a while until you straignten things out.