Hi Jeremy,
The first thing to check is that you are getting enough signal level to the PF. To do so, make sure that your PF is switched to instrument input. After that, are you playing chords or single notes? Are you playing a lot of out of key notes like g-natural in an E-MAJ scale (if you are you might want to switch to E-Chromatic)? Is the PF after a lot of distortion (it generally handles distortion quite well, but I'm curious as this might have an effect)? Finally, in difficult tracking situations it might help to add ~10 mS of delay to the shifted voice. You shouldn't have to do this, but it does make the pitch tracking a bit more robust.
Dan
