Not sure I can help. Seen this behaviour reported from previous Firmware and GroundControl versions but believe it is fixed in v1.03. Maybe it is worth a try to wipe the eeprom and rename the groundcontrol.ini in your home folder. This way you simulate a brand new user. Will search if I can find the posts.
See here: Calibration, Linkage, Alternate Sled Design
and Triangular Kinematics - Distance between sled mounting points