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I have been using Gnome Shell but recently tried working with Unity in 12.04. I have a couple of oddball apps whose tray icons don't work well regardless of theme (they must be missing transparency). Two apps Yammer and Jungledisk are the problem. If I can find the actual icons I could probably fix them. The icons in /usr/share/pixmaps don't match what I see in the tray. See the two icons right next to Skype.

enter image description here

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It is likely that you cannot just fix the pixmaps, but would have to fix the code in the application that sets the color for the background of the tray icon. A lot of applications have been reported with this kind of bug. You probably should add those applications if there hasn't been a fix already released for later releases.

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after a bunch of futzing with various them options, I managed to stabilize this... now if I could only figure out how to control indicator icon spacing :-) –  Kendor Feb 6 '13 at 0:10

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