There are certain cards that do not work across PCI-to-PCI bridges (which MXI-3 is based on). Cards that use serialized IRQs, require I/O space below 4KB, etc. Certain motion cards, specifically the PXI-7314 and PXI-7324, do not work with MXI-3 because they require I/O space which is not implemented in Win2000. I believe these two motion cards were updated to remove this problem. I am not sure if this is the issue you are seeing, since everything does work on one machine.
What do you mean by "system initialization fails"? Are you referring to the MXI-3 Optimization software?What happens when only the MXI-3 and the motion card are in the chassis? Does the system work with other operating systems?