Yes, this bug affects me also. I use a pop acount.

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https://bugs.launchpad.net/bugs/871568

Title:
  Removing spam does not clear flag

Status in “thunderbird” package in Ubuntu:
  Incomplete

Bug description:
  Steps to reproduce:

  1) Open thunderbird.
  2) Get 5 new messages (notice envelope indicator turning blue).
  3) Thunderbird automatically flags all 5 as spam. (which is correct)
  4) Go to Thunderbird menu, select Tools -> Delete mail as junk in folder. The 
5 new messages are now correctly deleted.
  5) Notice that envelope indicator is still blue, even though all new messages 
have been dealt with. Expected indicator to turn white.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: indicator-messages 0.5.0-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-12.19-generic 3.0.4
  Uname: Linux 3.0.0-12-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 1.23-0ubuntu2
  Architecture: amd64
  Date: Mon Oct 10 05:08:09 2011
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Alpha amd64 (20110802.1)
  SourcePackage: indicator-messages
  UpgradeStatus: No upgrade log present (probably fresh install)

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