Hi Nateman,
You can check if it is a resonance problem by simply adding a flywheel/mass to the stepper motor, if it is a resonance issue, then the ipm at which it occurs will change if you add mass. Have you run any calculations based on your drive train, including the mass and moment of inertia of all your components, I seem to remember that there was an excel spreadsheet that mad a fairly good approximation as to where resonance would occur and what the best driving parameters are likely to be considering all components, drop me a pm, to remind me, and I'll take a look to see if I still have a copy.
David
( never stop learning )
http://www.steamcastings.co.uk/