I ran into a similar issue with my PCIe attached to a 1045 chassis.
The system would boot but would not find the chassis nor would it find any of the cards installed in that chassis.
I spent hours trying to get this working, another 45 minutes with NI tech support and finally had the local NI sales rep come in and verify that it was an NI compatability issue between my Asus motherboard and the PCIe card. He was quite gracious and lent me his MXI-4 interface while I was exchanging my PCIe for a good old fashioned MXI-4 with NI.
The fix was to return the card to NI and go with the MXI-4 interface - this worked flawlessly from the minute I booted the system after installation. Everything came up and was recognized by the system and under MAX - as it should.
The Asus motherboard is a newer, up-to-date model and has a sweet PCIe video card that functions just fine. Asus is one of the most popular motherboard brands on the market so I am hard pressed to understand why this issue was a surprise to anyone. The problem, as I see it is that NI either does not know or is not admitting compatability issues with their HW.
A big help would be a listing on NI's site that lists 3rd party HW that does not function well with NI HW - this would have saved me days of aggravation and schedule slip.
I would recomend avoiding the PCIe interface all together until NI gets this issue under control or at least helps the development community out by listing HW that does not play so well with others.
