I am having having trouble with layers shifting while cutting multiple layers, not all the layers shift, some are fine, some shift left about .25’'. If I run each layer separately then everything is fine, so I don’t believe its mechanical. Any thoughts?
Well, everything I was about to suggest concerned mechanical backlash, but since you’ve ruled that out … 
Somewhere in the X axis drive, there is a loose setscrew allowing a shaft to turn just a little bit. For example, here’s a hard-fought problem that came down to 1/6 turn of a setscrew:
Everybody believes their problem can’t possibly be a mechanical problem. However, when the configuration hasn’t changed, that’s a clue the problem has nothing to do with the configuration.
Noise infiltration into a ruida controller over an inadequate USB cable can cause a jump that resets.
Pictures of what you’re seeing would be very helpful.
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Thanks for the input everyone @ednisley Good reminder to rule things out to quickly. The spindle does not have a set screw, I marked the top of the shaft and spindle, no slippage. Any other ways to troubleshoot the mechanical side?
@JohnJohn, I upload the file over me network and print from the controller. Its odd, the first three layers print just fine, then the fourth shifts. Also there has never been a shift mid print. Open to more suggestion.
Get out the hex wrench set, start at the motor pulley, and try to loosen each setscrew as you work your way to the laser head. The ones not giving you trouble will be nice and tight, the one letting the shaft move will be easily loosened.
If it’s on a shaft or coupler, rotate the shaft as you tighten the screw, so the screw ends up at the middle of the flat in the shaft when it’s firmly tightened.
If it’s holding a pulley or belt in place, shove whatever it was supposed to be securing into position, then tighten the screw.
That shows the fast motion from the position at the end of the third layer to the start of the fourth is energetic enough to trigger the problem. If it happens there, it will happen elsewhere: you just haven’t triggered it yet.
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