Comment 21 for bug 274461

gksudo is also transparent.

In my opinion the bug should be filed to the other apps which do not support transparency!
In this way you turned off the transparency support in the whole theme engine... So emesene, awn-manager and others won't have transparency anymore...

here's the list of apps supporting RGBA
http://www.cimitan.com/murrine/rgba-support/list

Anyway I also think that by default all apps should support transparency, but there should be a way to completely enable or disable RGBA on all apps in the apparence gnome app.
In the mean time how can I re-enable transparency in the ubuntu theme? thanks