One thing I didn't note anyone saying here is that it could be the capacitors on the motor as well.
Case in point, I had taken off my endbell and removed the screw and spring post so I could file off the nipple that was preventing me from getting my brushes aligned with the comm. In the process one of the mini caps fell out of the bottom and I didn't notice it.
I started a practice run and the thing was glitching like mad. Tried changing frequencies and rerouting wires to no avail. So in my case I took a step back to exam what had changed. Only thing that had was I was using a different motor. Went back to the old one an waalaa, smooth as silk. Took the glitching motor apart after asking around and getting that it could be a bad cap, and there was the gapping hole where a cap belonged! After digging around the pit towel I found it under my lathe. Put it back in place and again smooth as silk (driving not included
)
So, you might want to try another motor to see if that might cure your glitching as well. If so it just might be missing, or have a bad capacitor.
Scott