Almost the same here : I have many pop accounts in TB. They all end into
the tocal folders. Then I use filters to triage messages between
personnal / professionnal and other subfolders in each.

TB icon in unity launcher never shows number of new unread message if
they are in any subfolders. It only shows a number of new unread message
if those are not "filtered" though kept in the incoming local folder.

(Other side effect : pop up notification only display alert about "local
folder" instead of mail account being used since all my mail accounts
end in local folders (one global account), instead of each having its
own incoming/sent/trash folders (many accounts) - in other word, when I
had many separated accounts in TB, pop up alert displayed the name of
the one account concerned by new unread message. Errrr not sure if I'm
clear, my poor english sorry)

coeur-noir@CompaQ:~$ lsb_release -a
LSB Version: 
core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:cxx-3.0-amd64:cxx-3.0-noarch:cxx-3.1-amd64:cxx-3.1-noarch:cxx-3.2-amd64:cxx-3.2-noarch:cxx-4.0-amd64:cxx-4.0-noarch:desktop-3.1-amd64:desktop-3.1-noarch:desktop-3.2-amd64:desktop-3.2-noarch:desktop-4.0-amd64:desktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics-3.0-amd64:graphics-3.0-noarch:graphics-3.1-amd64:graphics-3.1-noarch:graphics-3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-3.2-amd64:printing-3.2-noarch:printing-4.0-amd64:printing-4.0-noarch:qt4-3.1-amd64:qt4-3.1-noarch
Distributor ID: Ubuntu
Description: Ubuntu 12.04 LTS
Release: 12.04
Codename: precise
coeur-noir@CompaQ:~$ uname -a
Linux CompaQ 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 UTC 2012 x86_64 
x86_64 x86_64 GNU/Linux
coeur-noir@CompaQ:~$ apt-cache policy thunderbird
thunderbird:
  Installé : 14.0+build1-0ubuntu0.12.04.1
  Candidat : 14.0+build1-0ubuntu0.12.04.1
 Table de version :
 *** 14.0+build1-0ubuntu0.12.04.1 0
        500 http://fr.archive.ubuntu.com/ubuntu/ precise-updates/main amd64 
Packages
        500 http://security.ubuntu.com/ubuntu/ precise-security/main amd64 
Packages
        500 http://ppa.launchpad.net/ubuntu-mozilla-security/ppa/ubuntu/ 
precise/main amd64 Packages
        100 /var/lib/dpkg/status
     11.0.1+build1-0ubuntu2 0
        500 http://fr.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

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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/856642

Title:
  launcher icon shows wrong number of new messages

Status in “thunderbird” package in Ubuntu:
  Confirmed

Bug description:
  The thunderbird launcher icon shows a seemingly-arbitrary number of
  unread messages. My inbox currently has 7 unread messages, and I have
  at least 500 unread messages in other folders according to the
  thunderbird UI. However the launcher icon currently shows there are 42
  unread messages. The number in the launcher icon does fluctuate, and
  it usually decrements when I read a message. It's never been correct
  about the number of unread messages, though.

  The Mail indicator in the panel also has a list of folders with unread
  messages, and a count of the number of unread messages in each of
  those folders. The unread counts in the indicator's listing are also
  inaccurate, and the sum of the unread messages in the indicator does
  not match the number of unread messages in the launcher icon.

  Thunderbird is configured for a pair of IMAP accounts. Each account
  has a number of folders and subfolders.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: thunderbird-globalmenu 7.0~b3+build1+nobinonly-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-11.18-generic 3.0.4
  Uname: Linux 3.0.0-11-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 1.23-0ubuntu1
  Architecture: amd64
  Date: Thu Sep 22 13:49:06 2011
  InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Beta amd64 (20100901.1)
  ProcEnviron:
   PATH=(custom, user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: thunderbird
  UpgradeStatus: Upgraded to oneiric on 2011-09-02 (20 days ago)

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