The problem looks a little bit confusing, but there is some information that you could use:
-The PCI interface controller chip should not be an issue, the PCI Bus has an international standard that both controllers should comply with it.
-The problem may be happening because of the way the resources are assigned, if changing the order the boards are inserted or installed in the system fixes the problems the there may be a resource conflict, you can go to the device manager in windows XP and try to change the resources that are assign to the device, this is set in the properties for the specific device.
-Another importat thing to verify is the version of the NI-DAQ driver, the most resent one is NI-DAQ 6.9.3. This can change the way resources are assigned.
If this problem persists then I would test the boards separately, inserting then one by one in the computer to see at what point the error gets generated. I hope this helps!