Thanks for the reply.
All images (lights, darks, flats, bias) were taken with overscan enabled. But whenever I try to calibrate any subs with a master (bias, flat, dark) I get the "Inconsistent overscan geometry" message.
I don't know if the problem is related to my overscan settings, or my masters. But the masters have the same pixel dimension as all subs. This is truly maddening.