I had the same problem, but all i had to do was turn off automatically joining my school network, remember my username and password, and every time i need to join the 802.1x select it in the airport on the menu bar and hit continues when it asks about the certificate...
This is really not an Apple problem. You should call your schools Help Desk or something, because their software is malfunctioning.
In my school all computers have to pass a compliancy test, for Windows machines that means running a virus scan, installing the latest patches, and all sorts of jumping trough hoops. For the rest of us on OSX, Linux or any flavor of UNIX, its just a quick act of plugging in the ethernet cord.