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?
 

This was the first thing I tried. And yes: without xen it does work (i
use the same kernel-config for xen2, and there pcix works also).
 

Unfortunately you can't just copy the config from the Xen2 kernel to the Xen3 
kernel: the PCI functionality that you saw in Xen 2 hasn't been *removed*, 
it's just been *moved* into Linux itself and out of Xen.
The Linux/Xen2 kernel config won't have the PCI quirk handling code because 
PCI quirks were handled by Xen itself. In Xen 3, Linux needs to have this 
enabled because Xen will not help it anymore.
Can you verify that any config options for your board that are enabled in your 
native Linux build are also enabled under the Xen 3-patched Linux kernel?