Most likely a shorted cable or a bad switch on the FU-3. Does the amp behave properly when with the F/S disconnected? If so you might want to try borrow another FU-3 and see if that takes care of it. If that solves the problem, I'd open up the controller and see if you see any obvious shorts or loose connections.
If it's not something obvious on the foot controller you probably need to take it to a MB repair shop. The guy who worked on my amp said that troubleshooting the channel switching mechanism a MK IV is major pain.
Sorry to hijack, but while you are on the topic of Mark IV footswitches, is there any easy way to replace the LEDs on the footswitch? Supposedly, the last owner of a Mark IV I might buy crushed the LEDs and never fixed them. I assume that they won't be wiggoled back into place, but will need to be completely replaced.