Comment 2 for bug 577427

Temporary Fix add this line to your excludes setting under the compiz manager:

(type=Desktop) | type=Desktop

Now you can get inverted windows straight after but and you do not have to logout and login again.

As a side note when you try to add setting to the excludes box you can capture the windows name for example but when you click okay the setting does not translate back to the main negative settings window. You get type= instread of type=Desktop. Desktop is being lost somewhere and not copied across.