Of course, the side trim pot needs to go all the way towards toe (0 setting).  I'm sure you've already tried that, but it's easy to accidently nudge it back.  I used to have that problem with my EV-5 and the PitchFactor.  I'd unplug it, then plug it back in, and re-calibrate it.  That seemed to work most of the time.  Occasionally, I'd need to cycle the power with it unplugged first.

I use that same EV-5 now into an EHX 8 Step Program, then out to my PitchFactor / H9.  After initial calibration, I set Pedal -> Pedal Calibration Disabled to YES in H9 Control.  I haven't had a problem since.  I'm not a big fan of the Pedal Lock setting (unless it's needed for a specific circumstance).  I haven't found the need to keep Pedal Lock engaged for the EV-5 as a permanent setting.