So I don't know for sure what the issue was, I think whoever set this system up when it arrived in shipping, connected everything in whatever order and had the PXI powered before the MXI chassis was connected. This would I think cause the BIOS to configure the PCI bus incorrectly. So I removed power entirely from the PXI and rebooted witht he MXI chassis already connected and powered.
But I also removed all software from the PXI controller and re-installed so it's possible the cause was somewhere there.
In either case, after doing the above two actions, the MXI chassis now is recognized in LV.
I saw my father do some work on a car once as a kid and I asked him "How did you know how to do that?" He responded "I didn't, I had to figure it out."