I have an update and will lead with a disclaimer: I have not posted these answers, because they do not, I repeat, THEY DO NOT work everytime. I have had this issue now multiple times and found a workaround everytime, but it has been a different one for each time the problem occured. I will integrate the two suggestions (below) into this "review of hacks", if you will:
Changing USB-cable -> didn't work (I figure it is a deep rooted software-issue)
Switching to a USB-hub -> didn't work -> happens both with a hub and without and also with other things plugged in and without
Updating windows (forcing update manually) -> worked once, when windows was way out of date (one month no updates) but had no effect other times
Downgrading Universal-Control -> worked twice -> downgrading to an earlier version (either by button inside the program or reinstallation of an older version) and then updating to the newest one again
Reinstalling Studio One -> didn't work -> I tried this every time, it never once worked, which makes me think, that this is a deep rooted driver related problem
Downgrading Studio One -> worked once -> tried this also every time (downgrading to an earlier version, where it worked), but since it never started after an update, it seems not to be related
Updating Studio One -> worked once -> also tried downgrading and then updating again every time..
My usual routine whenever it occurs is: 1. downngrading, then updating Universal Control, 2. Downgrading, then updating StudioOne, 3. Updating Windows, 4. Reinstalling StudioOne. That way I move from least to most invasive with the hopes of any of the earlier steps catching and fixing that bug. All in all I would still recommend the ATOM, but this is one heavily annoying (since it is reoccuring) problem. I hope this helps some, but like I said: It could be any of the above, but it could also happen that nothing works.
All the best
PS: Since this is only happening to so few people, I am actually beginning to think, that we have received faulty ATOMs