What I meant was, REF ALL HOME will reference all axis in sequence from where ever they are but if the axis was very near or at its switch, the movement would be slight. Thought that might have been what you were seeing.
If it happens from the Diag. screen, I would suspect it has something to do with the Shuttle Pro installation or plug-in.
Might try to disable the plugin to verify that it works properly just with the Mach screens. ?