I heard back from Colin regarding the speed setting in the config file. It looks like this was our problem, here is what Colin replied.

Hi Chadd,
Thank you for letting me know, I have changed the firmware and uploaded so everyone can download it. The firmware should have been as follows: #define HOMING_FEEDRATE {50*60, 50*60, 50, 0}. Those numbers are the speed at which each axis moves when it homes, if the Z speed is to high the two motors can get out of sync which causes everything to be out of whack.

Thanks
Colin