I have too used RepSnapper to generate gcode and I've seen this problem. it's an issue with the stl file and repsnapper interpreting it.
The way to spot if you have a bad stl/repsnapper model is: after you generate the gcode, if there are any yellow/purple streaks away from your model, thats where your printhead will end up trying to move.
I've moved on to using skeinforge for my gcode generation, while using RepSnapper to send it.