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Following is what's happening(plesae check the icon for show desktop/firefox/advanced setting on the top bar falling outside):

enter image description here

Can we do something about this?

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Are you using extensions? That does not seem to be the default gnome-shell appearance. – Alexandre Jan 26 '12 at 19:54
yup..lots of them :-) – subeh.sharma Jan 26 '12 at 20:02

This is fixed with version 4. You should now update, preferably by using E.G.O. The problem is I set the icon size to be too big in stylesheet.css. If you'd like to modify it, you only need to change the height to 22, in both places. The new version 4 will be available on Github & E.G.O very soon, and fixes several problems.

For everyone with the problem, press Alt+F2 and enter the following:

gnomesu gedit .local/share/gnome-shell/extensions/

Then, find and change the 'height' to a lesser value like 20/18/16/14 and then Ctrl+S to save, Alt+F2 and r to restart the shell.

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I encountered the problem beginning with v4. I installed it yesterday and then noticed the icon bleed over. I found that the height needed to be set to 16px for compatibility with gnome-shell themes that have very narrow top bars. Thank you for your work on this extension. – user45942 Feb 11 '12 at 13:03
This might be better as a comment to l300lvl's answer, especially since you are giving a different pixel size than them. – Tom Brossman Feb 11 '12 at 14:19
@Todd M: Thank you for reporting that. I will work this out eventually, but it would seem other extensions probably exhibit this behavior with themes like that as well, so you should use the report feature on E.G.O if you find any more errors. -Gratz. – l300lvl Feb 15 '12 at 3:12
up vote 2 down vote accepted

I found the issue myself. The "conflict" is happening when another extension named "Show Desktop Button" is active. Once i deactivated it, the icon size corrected itself...Weird!

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Don't forget to check this question as answered, once it is. – Gabriel Fair Feb 15 '12 at 3:47

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