Ok, Well, I have managed to get some strange behaviour, but not when moving a single SCM marker, only when selecting and moving two at once.
Your scheme for moving the VP markers is so complex, it is difficult to see whether there might be a problem in there somewhere. You could try a simpler scheme where you maintain the VP count in a Global Property, set the VP track up as an irregular grid with a region for each number, and use the ‘Send to Location - Named Region’ option to move the VP counter around.