Thanks guys. I pulled the pipe off and checked it; I can’t see any noticable bend when put against a straight edge; I would think it’d have to be fairly far off to be ~3mm off. I’ve put just the X axis of the gantry on, and it’s still off in the same direction. I took the frame apart, checked the conduit, put it back together, and re-measured and squared. Everything seems perfect square when measured, but it’s always off in the same manner. I’m completely stumped at this point what could be causing it.
I guess I’ll re-assemble everything and see if I can manually set it square enough before each cut.
RAGII – Thanks for the suggestion, but something else is going on with mine. I switched over to the new center design and the same problem followed me, plus even without my center assembly in place I see the same issue.