That machine seems pathetically underpowered to me. With tiny NEMA 17 motors run at 12v, it's amazing that it moves at all. But that said, try reducing the velocity to 100mm/min and acceleration to 10, and see if you're still losing steps. If so, cut it in half again, to 50 and 5. I know that's really slow, but if you can't move reliably there's no point in wasting material in the thing. Just out of curiosity, what does the company tell you about this? Did you ask them, or post your problem on their forum: Zen Toolworks LLC ? Index page ?
If you want to do more than crawl along, try giving it a higher-voltage power supply, assuming the drivers and arduino can handle it. If not, consider dumping that whole control system, replacing the 17-frame with 23-frame motors, replacing the 12-volt power supply with a 48v supply, replacing those infamous TB6550 drivers with a Gecko 540, and watch that little machine fly. Of course, once you do get it running, its lack of rigidity and other issues will probably make themselves known, but you can reuse the new control system on another frame you can buy or build yourself, and have a really useful machine...
Andrew Werby
ComputerSculpture.com ? Home Page for Discount Hardware & Software