I just cut a couple of large molds that are supposed to fit together, but they don’t. Not perfectly. When I align two corners and their edge, the other two corners are off. When I try to get those corners aligned, the others end up crooked. I found that the two supposedly rectangular halves are skewed just a little trapezoidal. The problem was the gantry plates were misaligned relative to one another. When the machine is off, they are free to move relative to one another by a good fraction of a centimeter. This skews the gantry relative to the Y axis, and everything you cut will be skewed the same way.
From now on, before I power up the machine, I will be adjusting the gantry.