Ok now I've come across an issue that I need clarification on. I'm using the exact same settings for speed, acceleration and jerk as Marlin had but my Y axis is skipping. Why would Marlin be able to handle these settings but Repetier cannot? Or am I missing something?
I thought it was the printer settings but now I think it's a communication issue. When laying down my purge strip before starting the print it just stopped and sat there then went to the x position like Y had kept going. X does not do it, just Y. So I have no clue what's going on.