Tenson I have just gone through this same senario for three weeks. I replaced the ballnut because it did not have enough bearings in it, Read my build log for why. Turns out that after chatting with dean it was all down to resonance and tuning the steps correctly. Try changing your steps to a lower figure, eg from 1/8 to 1/4. It may be a mechanical problem but this is worth checking. I went from 1/8 to 1/4 and it got worse. Then went to 1/5 and the machine is sweet!!

bruce