I've the same bug the mail isn't shown or visible in inbox when they're
a new mail. Perhaps because the mail is threaded and the first message
is read.

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https://bugs.launchpad.net/bugs/884288

Title:
  Message menu doesn't refresh new mail state for Thunderbird

Status in “thunderbird” package in Ubuntu:
  Confirmed

Bug description:
  If I open messages without clicking on the new mail icon in the panel,
  the icon stays blue, indicating that there's still new messages. The
  program should somehow check whether there's still unopened messages
  in the inbox.

  Ubuntu 11.10
  Thunderbird 7.0.1+build1+nobinonly-0ubuntu1 0
  notify-osd 0.9.32-0ubuntu3 0

  Bug summary: Notification menu should refresh when mail is opened
  without clicking on the message menu first. This doesn't happen.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: thunderbird 7.0.1+build1+nobinonly-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-12.20-generic 3.0.4
  Uname: Linux 3.0.0-12-generic x86_64
  NonfreeKernelModules: nvidia
  AddonCompatCheckDisabled: False
  AlsaVersion: Advanced Linux Sound Architecture Driver Version 1.0.24.
  ApportVersion: 1.23-0ubuntu3
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  david      5675 F.... pulseaudio
   /dev/snd/controlC0:  david      5675 F.... pulseaudio
  BuildID: 20110929183320
  CRDA: Error: [Errno 2] No such file or directory
  Card0.Amixer.info:
   Card hw:0 'SB'/'HDA ATI SB at 0xfe024000 irq 16'
     Mixer name : 'Realtek ALC889A'
     Components : 'HDA:10ec0885,1458a002,00100101'
     Controls      : 39
     Simple ctrls  : 22
  Card1.Amixer.info:
   Card hw:1 'NVidia'/'HDA NVidia at 0xfcffc000 irq 19'
     Mixer name : 'Nvidia GPU 14 HDMI/DP'
     Components : 'HDA:10de0014,10de0101,00100100'
     Controls      : 16
     Simple ctrls  : 4
  Channel: release
  Date: Mon Oct 31 09:42:23 2011
  ExecutablePath: /usr/lib/thunderbird-7.0.1/thunderbird-bin
  ForcedLayersAccel: False
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111011)
  IpRoute:
   default via 192.168.0.1 dev eth0  proto static 
   169.254.0.0/16 dev eth0  scope link  metric 1000 
   192.168.0.0/24 dev eth0  proto kernel  scope link  src 192.168.0.5  metric 1
  IwConfig:
   lo        no wireless extensions.
   
   eth0      no wireless extensions.
  LocalLibraries: 
/home/david/.thunderbird/6l6usuoc.default/extensions/{e2fda1a4-762b-4020-b5ad-a41df1933103}/components/Linux_x86_64-gcc3/libcalbasecomps.so
  Profiles: Profile0 (Default) - LastVersion=7.0.1/20110929183320 (Running)
  RfKill:
   
  RunningIncompatibleAddons: False
  SourcePackage: thunderbird
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 04/30/2008
  dmi.bios.vendor: Award Software International, Inc.
  dmi.bios.version: F4
  dmi.board.name: RS780-SB700
  dmi.board.version: Unknox
  dmi.chassis.type: 3
  dmi.chassis.vendor: Unknow
  dmi.chassis.version: Unknow
  dmi.modalias: 
dmi:bvnAwardSoftwareInternational,Inc.:bvrF4:bd04/30/2008:svnUnknow:pnUnknow:pvrUnknow:rvn:rnRS780-SB700:rvrUnknox:cvnUnknow:ct3:cvrUnknow:
  dmi.product.name: Unknow
  dmi.product.version: Unknow
  dmi.sys.vendor: Unknow

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