Thanks for the reply's.
Is the Z in your M92 correct now? If you use DWC and command the Z movement 100mm, how far does it move?
Yes I am pretty sure it is but I will double check that it moves 100mm when commanded.
That can happen if your steps / mm aren't easily divisible by your layer height.
For example, we had a 16T pulley on our Z stepper, belt driven to a 30T pulley. Since the math came out funny, every third layer or so was smooshed. We switched to a 16T / 32T pulley, our steps/mm are now 1 step = 0.01mm, and everything's happy.
I don't think this is an issue as the the leadscrews are T8's and should give me increments of 0.04mm (if my maths is correct).
Would print speed make a big difference on a small test print?