When I boot up Bitcoin Core on my Mac, the startup window (with Verifying blocks...) stays in front of any other open programs I have. After clicking on the Bitcoin window a few times it will go away, but then it cannot be found again (even though Bitcoin-Qt is still running). Also, if I enter Mission Control, the startup window disappears until I exit Mission Control, when it should be associated with Bitcoin-Qt. This is annoying as it interferes with any other work I am trying to do and occasionally the main Bitcoin Core window does not come up either. Sometimes after making the startup window go away, the main window will not come up, and I have to quit Bitcoin-Qt (which opens the quitting window) and rrestart without making the startup window disappear to have Bitcoin-Qt open normally.
Details: OS: OS X 10.9.5 Bitcoin-QT: v0.9.3.0-gcea5e49-beta
I'm not sure if this will be helpful at all, but Dogecoin-Qt works properly during startup, with the startup window being associated with Dogecoin-Qt in Mission Control and never covering other apps or disappearing altogether.