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I have upgraded my system with Xubuntu 14.04 LTS 64bit. I have installed the MediterraneanNight Theme by creating ~/.theme directory.

The theme works well although there is an issue with the indicator plugins under xfce4 panel:

enter image description here

Any idea why this is happening and how do I fix it?

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That's probably because the Indicator Plugin is actually the Unity Indicator Plugin (not Xfce) so I'm not sure it's possible to get it to integrate properly unless if you can program themes... If you are able to sacrifice the indicators and would rather have a fully themed top bar you can try the 'Notification Area' Item to do a similar job. –  Ads20000 Apr 22 at 12:45
    
For compatibility with Unity indicators the indicator plugin uses Gtk3. And since the panel and all other plugins use Gtk2 many themes have not yet been updated to support Gtk3. –  Andrzej Apr 24 at 7:29
    
If you like this theme I recommend contacting its authors and asking if they can support Gtk3 in Xfce panel. You can also switch to a few updated themes (mostly the ones shipped with the default installation of Xubuntu). –  Andrzej Apr 24 at 7:37

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