I have a tyan mainboard with an AMD-8131 PCI-X Bridge.
With xen3-testing all PCI-X devices behind that bridge (and the bridge
itself) are invisible to the xen0 kernel (in lspci).
With xen2-testing it works.
I greped the sources for 'AMD-8131' and '8131' and found that xen3 does
not contain something, but xen2 seem to have something in it, so that it
detects that PCI-X Bridge.
 

Upsie, We were planning on buying one of those thingies, too (for use with 
xen), with quad dual-core opterons, tons of RAM, and PCI-X Adaptecs to 
connect the external RAIDs...
Looks like we better wait a bit, then.
For the 2.0->3.0 changes you mentioned: I think thats because xen3 now doesn't 
do much hardware initialization itself, instead relies on dom0 to do so.
Did you check the dom0 kernel config if it contains the neccessary functions?
If you create a non-xen kernel with the same config (copy the .config into a 
vanilla kernel dir, run make oldconfig), does that one work with PCI-X?