I have researched and found a couple of similar cases as yours, but with different devices. It does seem to be an issue with the USB devices, which would explain why the PCI version of your device works fine.
I would suggest upgrading to the latest version of the DAQmx drivers. A lot of times issues like these are fixed in newer versions of the driver. You can download the latest version from the following link.
NI-DAQmx 8.6.1 - Windows 2000/Vista x64/Vista x86/XP
http://joule.ni.com/nidu/cds/view/p/id/950/lang/enWhat type of processor are you using? I did see a few issues with USB related to AMD processors.
Also, can you try logging in as Administrator on each restart? Does the problem still persist?
Please try these suggestions and update me of the results. In the mean time I will try and replicate the issue on my end.
Regards,
Chris Delvizis
National Instruments