Hey Jim, hey Bill, hey all,
this is true, it can happen at any time. Usually it depends on how a gantry machine homes. A gantry-style CNC is one with two Y rails. Often the machine only “homes” one of the Y axes. Theroretically it is possible if your machine is a parallelogram, the two Y carriages could alter their home position in a way that the resulting angle is a right angle even if the X and the Y axes form no rectangle, but a parallelogram (software squaring)
Anyway on the buildbotics-derived Onefinity Controller, it can be remedied this way