Have you tried to run the program as administrator?
With earlier versions of WBFS manager, I remember I had to disable User Accounts somewhere in the control panel, to get it to work. I don't have to do that anymore though.
Assuming you still have the U3 partition on it.. You can try removing that, I know I had some trouble using mine to play movies on geexbox. taking out the U3 fixed all my problems.