I wanted to follow up on this now that NI-VXI 3.5 is available. Although this release is specifically for the VXI-USB, it does work on PCI-MXI-2 and has a few minor changes in Resman and other code that might fix this problem. Since it's not clear what specifically was going wrong with your 3.3.1 installation, I can't guarantee anything, but you might want to give 3.5 a shot and see how it goes. Please note, however, that NI-VXI 3.3.1 is the recommended driver for PCI-MXI-2 systems generally.
-Scot