This item is from the Yet Another Enhanced IDE/Fast-ATA/ATA-2 FAQ, by John Wehman and Peter den Haan with numerous contributions by others. (v1.92).
There is a problem with PCI and multi-I/O or dual-ported IDE interfaces. Such interfaces need two or more predetermined interrupts which cannot be shared with other PCI devices, which is probably impossible with your PCI slots. The usual workaround consists of either integration of I/O functions on the mainboard, or the use of a tiny 'paddle' board that plugs into an ISA slot.
This is not so much a weakness in the design of PCI, but a conflict between PCI's plug'n'play philosophy and the requirement that these interfaces be fully compatible with oldfashioned I/O cards.
Some vendors use PCI interfaces that rely on a proprietary extension of the PCI bus. This is obviously not portable; you often can't even move the card to a different slot in the same machine. Moreover, such extensions may cause compatibility problems since they use PCI signals reserved for other purposes.