Just to ask the obvious (and NOT intended to be insulting), are you sure you aren't dropping a few feet during the SS?
The Atom Safety Stop feature is a bit complicated, since it has a couple of different options for how you can set it to work.
In one mode, if you get within 5' of the stop depth, the SS starts. If you drop to 10' below the stop depth, it stops. So, if you only drop 5' from when the stop initially starts, the SS countdown could stop.
In the other mode, once you ascend to 20' the timer starts. If you drop below 30' for 10 seconds, it stops.
If you are holding your depth, then, well, it sounds like it's broken.... Fortunately, the Atom comes with a 2 year warranty (to the original owner).