The diff files should be self explanatory. This actually fixes bug #11976, I use the same setup and it was pretty annoying.
The first change comments out that #if 0, which I don't understand why it was there in the first place (that's why I commented it and didn't just erase). The only reason I can think of why it's there is because it doesn't work everywhere, but I can't think of any cases (if GSAppOwnsMiniwindow == NO wouldn't _counterpart = 0?).
The second change is pretty obvious. If a window is minimized it needs to be ordered out.
I think these changes are correct and should work everywhere.
On anther note, I'm still having problems with certain apps not quitting (SystemPreferences and ProjectCenter) when they are told to terminate, be it using GWorkspace's Logout and the apps Quit menu option. As always, I have no idea why!
gui.diff