When I first got my TimeFactor, I plugged in my Boss FS-5U switch into the aux jack and it worked for tap tempo. That's exactly what I wanted. With the 2.0 update, the aux switch sets turns RPT (repeats) off and on. I changed the aux switch setting to TAP and saved but it still triggers RPT.
Found the answer to my own question. They added the ability for the aux switch to control the three onboard buttons. By default these are set. I ended up having two functions assigned to my aux switch and RPT won out. The solution is to clear the extra switch assignment.