I've posted this link because it almost exactly resembles my symptoms. Except, i run windows 7. To be more specific, it seems to only be the USB 2.0 slots that fail. the 3.0 Slots continue to work fine. In fact, the front 2.0 slots wired to the board work fine as well.
There was a link posted in the above article to microsofts website with a hotfix for vista.