We would agree that the saving should not become "dirty" unless something changed. If you can reliably recreated this behavior while making certain that nothing has changed, no window has moved or resized or anything else, make a tech support ticket with the steps to recreate, make sure to include your operating system version and Studio One version and tech support will look into it.
It may well be some small parameter changing that you didn't notice if using a control surface or similar, hard to say.
