I agree with Hood. Im a complete newbie though, so it may not be worth much.
Try going into the config drop down. Then, clicking on motor tuning.
Then, cut your acceleration in half of what you have listed on each axis and drop the velocity down to about 2/3 of what its set at now. Leave the steps alone.
Then, try repeating the problematic action. If it cures it, your motor settings were too optimistic. I've read you should set your motors at about 80% of what they are listed. Ive slowed mine down to about 20% of max because everything is moving faster than I can handle right now (my confidence anyways.)