by the sounds of it its not a case of clearing a fault its still got one - needs to see what fault is logged and then go from there really...
If the fault is stored in the memory, is'nt this still there until cleared even if the, lets say it was something unplugged but now plugged in so fault not there anymore but fault still logged?
Or does it clear the fault once the offending item is plugged back in?
On an old diesel alfa of mine, if you hit 4.5k revs an EGR fault made the engine light come on and go into limp mode, turning off the car and back on allowed the car to get full power again but the engine light was still lit until i plugged this machine in and cleared the fault.