Nope. That has nothing to do with it. On my machine it is disabled, as in earlier versions where cubase kept playing while switching windows.
I must say that I havent had the problem since I posted the bug, and the only difference since then is, that I am working on a new project which is created in 9.0.1 (earlier it was a 8.5 project). But again the problem didn’t happen often, so I am not sure it is gone after working on the new project yet.