If your atomic 2nd has a venturi adjust vane, you can try setting it to the minimum position and see if it still does it.
The venturi adjust was cranked down to the minimum, which got me wondering.
There is no manual venturi adjustment on the Atomics. The venturi adjustment is automatic, via the AFC, which reduces the venturi assist when at the surface and "turns it on" once you are under pressure. So when you did this on land, the venturi effect was already turned down.
What you did adjust was the cracking pressure adjustment, which will have an effect, but less than the venturi effect.
You could also have your shop adjust the intermediate pressure on the 1st stage up a bit.
Adjusting IP on the Atomics requires the first stage to be disassembled, with shims being put in or removed. If you were to do this, it is almost an overhaul, so might as well do a full overhaul. Also, I think IP problems will mostly evince itself with bubbling at rest, rather than like this.
OP, if you depressed the second stage cover a lot, then it is pretty normal for them to continue to freeflow until some back pressure is applied. If you only pressed it a little and it still happened, my guess is that you need some lubrication in the second stage balance chamber o-ring. (the one on the poppet)
But again, if it only happens when it's pressed in a lot, I'd say it's normal.