my mendel is calibrated and yet, i did something to the firmware that caused the following weirdness: the very first movement, when sent to the x&y stepper motors, is wrong / off by a small distance. after that initial movement however, it all snaps back to the calibrated distance for all movement thereafter. the first movement of the x-axis falls short slightly and the y-axis grows. for instance, if i jog the y-axis in 10mm increments, the first 10mm turns out to be actually 11.5mm or 12mm... then, the second 10mm jog (and all thereafter) produces the calibrated exact 10mm. again for example, when i print the 20mm test cube, i end up with something more rectangular.
