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It sounds like infamous "ribbon cable" issue. There is a ribbon cable that connects the main circuit board to the circuit board attached to the parameter pots. Reseating the cable has fixed the problem for many people. I recently did this as I was having issues with both a modfactor and Pitchfactor. Haven't had any issues since, but I also haven't had any extended playing time since doing it.
It does, of course, require you to open up your unit, which I'm guessing voids any warranty and is most likely discouraged by Eventide. You would need to remove the knobs, 4 Allen screws on top, 5 screws in the bottom, and screws that hold the two circuit boards together. If you decide to do this, be careful! Nothing worse than permanently busted hardware.
Joe (he who waits for Factor updates)