I have this problem as well. Windows 8.1 x64, TrackIR 5, XBOX 360 wired controller. The XBOX controller dissappears when going to Configure --> Controls. It seems to work OK as long as I don't have to open this configuration to change something (enable / disable / nullzones or keymap).

To clarify - for me it seems that it's the actual opening of the Configure --> Controls menu that resets the controller. Up until that moment, everything seems to work okay.