I think the PCI was only ever tested from the Firmware, but it did work (on
rev 5s anyway, some earlier revs needed a mod). I thought it was part of the
initialization the firmware did. Did you check the device tree?

I know there were some issues with the VIA chip, I think you had to do some
incantation before it worked. Did you read the notes and VIA app note on the
hardware page?
http://www.research.digital.com/SRC/iag/info/dnaext/hardrev5.html

Im afraid its long enough ago that its a bit fuzzy now!

Mark