Yep - I stumbled on this one too. I am a bit new to Cubase (have used the LE versions, but started using Cubase Artist really seriously a while ago), and my initial thought was that I had overseen some crucial setting somewhere. After a lot of searching I had to conclude that was not the case.
While I really like Cubase (I am planning to upgrade to the “full” version in a few months), I think this behaviour is the most annoying thing that is present in the program. My “work-around” is to not fully maximise the window, but “fill up” all the available space with the “floating” window. In that case you do not loose the full sight on your work when you open a “wrong” window (one that cannot be made “always on top”). This takes some space unfortunately, and you are left with less space to view your tracks.
Like I said… it wont drive me away from Cubase -far from it-, but I would not mind a bit if this “feature” gets some ehhh… “correction”…