Jeffrey,
This post may come too late for you, but are several reasons you might see this type of behavior:
1. The grub screw on your pulley(s) may not be tightened, causing your motor shaft to slip.
2. Your belt(s) may not be tight enough, causing your pulley to "skip" over steps in the belt
3. Your acceleration numbers may be too high, causing your motor to fall behind
4. As jbernardis mentioned, you may need to dial up the current being applied to your motor