Yeah, I think Cubase is partly to blame here.
I mean, aways on Top doesn't really mean "Always".
Even if you switch to any another running app (Finder for instance), you will see that the "always on top" window still disappears.
Seems to be exactly what happens when the BBM4.app throws up a yellow note, it tries to come to the foreground, sending Cubase to the background.
It would either be nice to be able to either suppress the messages, or have BBM4.app not try to take the focus when it generates a message.
It's funny how the AU in Logic/ GarageBand don't seem to be affected by this at all.