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.