Running the ClearPath motors in quadrature mode is free, same wiring and everything. AFAIK there are only upsides to doing so- your fastest signal becomes half as fast, so you gain margin, and noise is less likely to accumulate into "permanent" errors, more likely to jitter back/forth one step. Which is still bad, but less bad.
Even if that has nothing to do with anything you're experiencing, I'd still advocate for it as technically better.
