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When I use CheckGMail, it shows up in Notification Area. But it never use gnome-panel's background color. It looks like something wrong with the panel.

Same goes with aMSN.

Is there a way to fix it? Or change theme to cover this up. I am now using Elementary theme.

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New version of CheckGMail (from PPA or in "check updates" command from tray icon menu), as far as I know, have that bug fixed.

BTW, gmail-notify have nicer integration with app-indicators. Try it.

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This is a known bug of aMSN: – DrKenobi Nov 9 '10 at 0:49
I don't use aMSN, sorry.. – Extender Nov 9 '10 at 5:59

Change ur panel background color until they fix the bug. Just delete or rename panel.png in /usr/share/themes/elementary/gtk-2.0 and you will be able to change the color of your panel.

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You could use gmail-notify as Extender said, but you should also switch to emesene, instead of amsn, because amsn is almost dead (still under development, but going so slow you don't get a release for months).

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