From Fab@Home to Repstrap... but with a tracking issue.

So for the last year I have been working on transforming an inoperable Fab@Home (http://www.fabathome.org/) to a RepStrap. I used the structure and motors from the Fab@Home but I swapped the control board out for a RAMPS 1.4 with Arduino Mega 2560 using Pololu drivers. For software I am using Sprinter with Pronterface. I am having some issues though with the tracking of the printer head. Everything has been properly calibrated and works well in manual mode. However, when attempting to print a part it displays correctly on the virtual build platform through Pronterface. When I try to print though it makes some very odd shapes that don't resemble the actual part in any shape or form. I removed the hot end and attached a pen to track the actual movement. In the picture attached I attempted to print a 10mmx10mmx1.2mm square. I have been trying to figure out what the problem could be for a while now and can't seem to figure out the issue. If anyone could lend some help or advice I would greatly appreciate it, I am at a total loss now.