If you have your heights set up accurately, where do you have your part located in the actual set up? Fusion automatically sets the part in the centre of the stock and you have to change it manually. If correct...

How are you setting your Z height? If using the Z setter I tested that quite a bit one day and got errors anywhere up to 0.3mm even using a slowed down double probing routine, its just not consistent for some reason, or at least mine isn't anyway. I don't use it anymore and touch off with a feeler gauge which takes a little longer but is far more accurate and repeatable.

Also the original hollow panel OMIO bed is a block of turd to put it lightly, putting a sheet of A4 paper on it will probably cause it to deflect. Getting smooth top surfaces and accurate heights is nigh on impossible, so expect to see a bit of error. I got a big slab of aluminium tooling plate to replace it and the improvement is massive. The last part I made was meant to be 12.55mm high and came out at 12.54mm with both surfaces flat to within 0.00mm and smooth to the touch. An impossible task on the original bed, its an addition worth its weight in gold imo, well worth looking in to.