I just finished (all but my extruder) building my prusa i3. Everything is running well except for z axis homing. It sounds terribly noisy. The odd thing is though, if I send say a G1 Z50 code from repetier it sounds just as one would expect and moves quite smoothly. I can use repetier to move it up and down in increments of .1, 1, or 10 mm and it s great.

If I tell Z to go home from repetier it sounds awful. The same thing happens even if I move a millimeter using the graphical LCD controller. I have a feeling this is some type of software issue since the Z axis works well when controlled with Repetier (exept when homing in repetier). What might the issue be? I am using Marlin with a standard Prusa i3 rework build.