Why doesn't side two line up when I flip my double-sided job?

Why this happens

Any positioning error doubles when you flip. If your registration is 1/16" off, the two sides disagree by 1/8". Sources of that error:

1. Index or dowel holes not symmetric about the flip axis.
2. Flipping about a different axis than the one set in Job Setup (flip horizontally vs end-over-end matters).
3. Gantry out of square: X and Y are not truly perpendicular, so the flipped coordinate frame does not mirror cleanly.
4. Sloppy dowel fit (undersized pins in oversized holes).

The fix: dowel pin registration

1. On side 1, drill registration holes through the workpiece and into the spoilboard (a Drilling toolpath in the same file guarantees they are in the machine's coordinate frame).
2. Place the holes in scrap margin, mirrored about the flip axis ("flip about job center" symmetric).
3. Insert snug dowel pins, flip the board about the same axis selected in Job Setup, drop it over the pins, and cut side 2 without re-zeroing XY.
4. If misalignment persists, square the machine: measure both diagonals of a large cut rectangle. Unequal diagonals mean an out-of-square gantry.

Pro tips

• Snug pin fit matters. Drill holes exactly at dowel diameter (test in scrap, tap fit, not drop fit).
• Expect residual error to read doubled. Measure the actual offset, halve it, and that is your registration error to hunt.
• Alignment quality is set the moment you drill the holes. Nothing done on side 2 can recover bad side-1 registration.