You should probably ignore my previous comments, since my brain has turned to mush over the holidays.
Current thinking is that the main relevant difference between the H9 and the Factors is that the former has a combined pedal/switch jack. As a result, you have to tell it which one you want it to be. To further complicate things, this did not work too well in earlier software.
I would suggest that first you make sure that you have the latest software. Then, in system mode, make sure that UTILITY/EXPTIP is set to SWITCH. This is essentially what Greg is saying above.
My guess is that this will fix it. If not, get in touch.
