So the end result with me was just that I was expecting the left motor to want to extend after calibration, so I was positioning the left chain back to the top tooth of the sprocket and clicking “extend chain”. However, the extend in this case really means “retract”, because the software is expecting that I’ve left the chain extended all the way to the right motor for the previous measurement. Once I realized that, I’ve been able to calibrate correctly by just remembering that the extend in this case means retract