Unfortunately, on some machines, due to how the holes are cut in the plates, and the powder coating applied and the extrusion is tapped things, while within the tolerance specification, aren’t as true or square as one would like — the larger machines magnify even the smallest of not quite right dimensions. Things to try:
- adjusting the Delrin V-wheels on the gantry end plates — the top set of holes should determine the relationship, but sometimes one isn’t aligned at the top of the hole
- rotate the spindle mount 180 degrees — this is a long shot, it’s usually quite squarely machined, but check and see if this changes things — if it does, contact support w/ how much
- swap the extrusion end-for-end — this could make it worse, but is still worth trying
- check the washers on the Delrin V-wheels — also check that the Delrin V-wheels are within spec and have the appropriate size spacers — a few folks have replaced the regular washers w/ precision shims of various thickness to ensure that everything comes out perfectly to the same dimension
- file or drill out the holes in the end plates as necessary
The big thing is, start with one reference — say by leveling the machine front to back and side to side, then check, and if necessary loosen and adjust the next connected part to make it square and plumb in relation to the reference — continue that until one gets to the spindle carriage.
Sometimes one winds up chasing one’s tail — and adjustment at some point seems to make some other measurement worse — it can be maddening — best to start w/ the largest adjustments and work one’s way down to the smallest. Also don’t keep track of how many times you tear down and re-build the machine, and above all, don’t let your significant other count such efforts.