Here we are in 2016 & this unit is still doing this behavior, albeit very intermittently.
It sounds like the ribbon cable that connects the TimeFactor’s top and bottom boards might be loose. If you write email@example.com, they could give you instructions for reseating that if you feel confident opening it up and doing that. Alternatively, you could send it in to Eventide to be repaired for a flat fee which will be much less than the $400 you mentioned for a new unit.
I’ll write them and reference this thread. I think I can open the unit myself and see if it gets fixed.