I have found a solution. I have deleted a folder /home/myname/.config/indicators/ and now it is working fine. But I think that it is still a bug. Because, it can be a problem when upgrading from 12.04.1 to 12.10. In my case I have installed 12.10 without any changes in my /home/ folder, because it is on a different partition.
-- You received this bug notification because you are a member of Desktop Packages, which is subscribed to thunderbird in Ubuntu. https://bugs.launchpad.net/bugs/1062746 Title: indicator-messages don't show new messages from Thunderbird Status in “thunderbird” package in Ubuntu: New Bug description: Indicator-messages don't show new messages from Thunderbird like in 12.04. It is not getting blue also. ProblemType: Bug DistroRelease: Ubuntu 12.10 Package: indicator-messages 12.10.4-0ubuntu1 ProcVersionSignature: Ubuntu 3.5.0-17.27-generic 3.5.5 Uname: Linux 3.5.0-17-generic x86_64 NonfreeKernelModules: nvidia ApportVersion: 2.6.1-0ubuntu1 Architecture: amd64 Date: Sat Oct 6 12:36:37 2012 InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Beta amd64 (20120929) ProcEnviron: LANGUAGE=ru_UA:ru PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=ru_UA.UTF-8 SHELL=/bin/bash SourcePackage: indicator-messages UpgradeStatus: No upgrade log present (probably fresh install) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/thunderbird/+bug/1062746/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : [email protected] Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp

