Hi Dab - The steppers will never by perfect in sync mechanically. When they are initiated they find the closest magnetic coil to their stationary position. One may go clockwise to this position the other anticlockwise, vice versa or they could be close. All depends on how and where they were shut down and how much "spring" is in the mechanical system as a whole.. This is the clunk on initiation. To fix this a home position is needed that can realign them to the mechanically correct position. If the clunk is severe and the gantry moves a lot at initialisation this means the structure maybe "sprung" or is poorly aligned. So firstly work through the structure and check its not loose, misaligned or twisted or whatever. A clue to this is if the system is off and you push one side of the ganty and it proceeds but the other side lags then you need to stiffen the gantry structure.

Another thing to try is to manually move the gantry to its stops (if you can do this depends on your drive system) and physically hold it to them at start up. This removes the compliance of the start up and they may sync better...if you can't do this manually then do it via software control then shut down and restart may learn something about the issue...or clamp them in place before startup...or clamp one and se what the other does etc Cheers Peter

You say one motor is in sync with the other? Is one "slaved" to the other in the controller? or are they being driven from one controller in parallel or series? cheers