It sounds like you have a problem either with your cable or your expression pedal.  I just hooked up a Roland EV-5 to a TimeFactor with the latest release installed on it, and after going through the calibration steps I described above, it's working fine.

I didn't realize that on the FAQ it says the expression pedal can be up to 20kohms.  Else where we've said up to 25kohms. I think the Ernie Ball expression pedal was recommended on the FAQ simply because it works and is constructed of sturdy materials that should be able to take a lot of abuse on the road.

The M-Audio pedal you mentioned will also work fine.  (I just hooked one up to the TimeFactor…) It has a switch on the bottom of it that has to be set to the correct position though for it to work; it has to be set to the position labeled "M-Audio".