The possible culprits are:
- hole positions / powder coat on the end plates — sometimes they’ll be off in opposite directions on pairs of plates, and compounding that (of course) the powder coat will be thicker at the top of one hole, and bottom of the other
- extrusion not cut squarely
- V wheels are different diameters — this hasn’t been as much of an issue for a long while, mentioned only for completeness’ sake
Most likely it’s a perfect storm of each thing adding up — time was we’d suggest flipping the extrusion, but if you have the nifty decal, that’s not an option. Things to try:
- clear the powder coat out of the (EDIT: top) holes (don’t enlarge them into the metal)
- shim the ends of the extrusion
- file / machine the ends of the extrusion square — this is easiest if one pulls all the rails, stacks them, and uses a large fine file to draw file them after marking the high points w/ a marker
- swap the V wheels around
See https://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine#Squaring_the_Machine