Thanks for the suggestion. I originally didn't use acceleration. I just tested it with acceleration and that seemed to fix the problem.
I'm not sure I have any alternative to the boost converter. I have to run this on a 12vdc electrical system and I need a minimum of 24v for the driver. I'm running the booster output at 36v right now, but may move that higher if need be. Here's a link to the booster I bought:
http://www.ebay.com/itm/DC-DC-600W-10-60V-to-12-80V-Boost-Converter-Step-up-Module-Power-Supply-/170893208817. I thought it would be enough to run one stepper. My stepper is a 425 oz-in and the specs are
http://www.buildyourcnc.com/Documents/PN.SM60HT86-2008BF-U%20%28inhouse%20PN.60BYGH303-13%29%20%281%29.pdf. I have it wired in bipolar parallel.
Do you still think the boost converter I have is not the way to go? Is there an alternative that I can make work with my 12v system?
I think the faster the RPM the better. Maybe a bit over 1000rpm. I think I was at 120 rpm with the 10 microstepping, so full steps should be ok. I'm not as worried about being low on torque because I think the DC motor this is going to replace didn't have much of a torque rating.