Obviously, this shouldn't happen. It may be that for unknown reasons the GC is deluging the TF with MIDI messages and is clogging its pipes. Or maybe there is something (again unknown) wrong with the TF.
It might be helpful to know EXACTLY what the TF display is showing during the 2-3 seconds. Also, if possible, beg borrow or steal a different controller and see if you get the same result.