What am I
doing wrong? I've had no problems with any of the algos before. Are the
Pitchfactor algo's so much louder than the other algos?
I don't think you want to turn up the gain in the line in menu within the pedal. You probably should turn that back down to where it's not clipping and turn up the master volume on your amp so you're at the same level as you were before.
PitchFactor's algorithms are not necessarily louder than other algorithms, but different algorithms have different gain structures. And if you go into Octaver for example with a signal that already has a lot of bass, that's going to clip sooner than sending the same signal into a reverb.