Dear Mr. Dawson,
I have started using FSUIPC for axis and button assignment only a couple of days ago. Everything works fine, except that I'm experiencing the same issue with a stuck rudder.
I'm using a Saitek Pro Flight Yoke System with Throttle Quadrant in combination with a pair of rather old CH pedals. Controllers are deactivated in FSX, axis assigned through FSUIPC.
Regardless of whether I connect the pedals directly to a free USB port or through the Saitek yoke functioning as a USB hub, after a certain time (I figure around 30 to 45 minutes), the rudder will suddenly cease to work. Only after accessing FSUIPC via the Add-Ons menu and immediately leaving it again, will they reverse to functioning. Power management for all USB ports is turned off.
I would be glad if you have any more ideas as to what might be wrong here...
Regards,
Oliver