What's the mod wheel/aftertouch set to modulate?
If either's set to cutoff, and it somehow receives a stray message, it could open up the filter and make it appear to not work.
The mod wheel and aftertouch can add so much to the cutoff input voltage (I believe they can fully open the filter when the knob is set to fully closed), that if they get set to the max value, it will always be at the top of the audible range.