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[Sean Fitzpatrick <sean.fitzpatrick@xxxxxxxxxxx>]

Problem solved in my case: I kept the settings for Thunderbird from my 11.04 install, and just noticed that the old add-on to provide notifications via Ubuntu's notification system (which has been superseded in 11.10) was not disabled.
Disabling 'Messaging Menu and Unity Launcher Integration 0.8.2' resolved the problem for me, since this has been replaced by 'Global Menu Bar Integration 2.0.1'. I'm going to go ahead and mark this as invalid since the 'bug' seems to be a configuration problem in each case.
However... it does remain true that people using Thunderbird in 11.04 who upgrade (or keep their /home directory in a clean install) may experience problems, and may not find their way to this report. (On the other hand, if you figured out how to integrate Thunderbird with Unity in 11.04, you'll probably figure out what's wrong, as we all apparently have!)

** Changed in: thunderbird (Ubuntu)
       Status: Confirmed => Invalid

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https://bugs.launchpad.net/bugs/845436

Title:
  Missing new email notifications in oneiric

Status in “thunderbird” package in Ubuntu:
  Invalid

Bug description:
  When a new email is received, the "me" icon turns blue, but I don't
  get any new email notification bubble, contrarily to what happened
  with natty.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: thunderbird 7.0~b2+build2+nobinonly1-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-10.16-generic 3.0.4
  Uname: Linux 3.0.0-10-generic x86_64
  NonfreeKernelModules: fglrx
  AddonCompatCheckDisabled: False
  AlsaVersion: Advanced Linux Sound Architecture Driver Version 1.0.24.
  Architecture: amd64
  ArecordDevices:
   **** List of CAPTURE Hardware Devices ****
   card 0: Intel [HDA Intel], device 0: AD198x Analog [AD198x Analog]
     Subdevices: 2/2
     Subdevice #0: subdevice #0
     Subdevice #1: subdevice #1
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  daniel.arteaga   1829 F.... pulseaudio
  BuildID: 20110906004732
  CRDA: Error: [Errno 2] El fitxer o directori no existeix
  Card0.Amixer.info:
   Card hw:0 'Intel'/'HDA Intel at 0xfebdc000 irq 49'
     Mixer name	: 'Analog Devices AD1984A'
     Components	: 'HDA:11d4194a,1028027f,00100400'
     Controls      : 34
     Simple ctrls  : 20
  Channel: default
  Date: Fri Sep  9 10:18:36 2011
  ForcedLayersAccel: False
  IfupdownConfig:
   auto lo
   iface lo inet loopback
  InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Release amd64 (20110427.1)
  IpRoute:
   default via 84.88.76.129 dev eth0  proto static 
   84.88.76.0/24 dev eth0  proto kernel  scope link  src 84.88.76.28 
   169.254.0.0/16 dev eth0  scope link  metric 1000
  IwConfig:
   lo        no wireless extensions.
   
   eth0      no wireless extensions.
  ProcEnviron:
   LANGUAGE=ca:es_ES:en_US:en
   PATH=(custom, user)
   LANG=ca_ES.utf8
   LC_MESSAGES=ca_ES.UTF-8
   SHELL=/bin/bash
  Profiles: Profile0 (Default) - LastVersion=7.0/20110906004732 (Running)
  RfKill:
   
  RunningIncompatibleAddons: False
  SourcePackage: thunderbird
  UpgradeStatus: Upgraded to oneiric on 2011-09-06 (2 days ago)
  dmi.bios.date: 02/18/2009
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A02
  dmi.board.name: 0F373D
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A00
  dmi.chassis.type: 15
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: dmi:bvnDellInc.:bvrA02:bd02/18/2009:svnDellInc.:pnOptiPlex760:pvr:rvnDellInc.:rn0F373D:rvrA00:cvnDellInc.:ct15:cvr:
  dmi.product.name: OptiPlex 760
  dmi.sys.vendor: Dell Inc.

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