I think one of the major PCI issues with newer cards and classic amigas is that most classical PCI "Bus Boards" slots are only pci 2.1 compatible. If memory serves, PCI 2.1 will not provide a low power voltage line that PCI 2.2 cards require.
If I remember correctly Elbox fixed the PCI 2.2 issue with one of their amiga 1200 PCI busboards
