Here is how it turned out:

So, it would appear the problem is either in my electronics, or my mechanics.
Does anyone know any guides that could help me narrow down the problem? Or any gcode/tests I can run to help?
Is it possible microstepping could be playing a part in this? I have the controller (Pre-made, generic 4 axis board) set on 1/8 microstepping. I really do like it as it makes everything a lot quieter and smoother, not to mention more accurate, but if its causing me problems I may need to find another solution. But I'm was under the impression almost everyone used mcirostepping without problems?
I built this whole machine myself, and this teeny little glitch is all thats stopping me from finally completing it.
If hi res, detail pictures of the machine will help, I'm ready with the camera.
Cheers,
Dan