I have the same problem on jabber (XMPP).

First time somebody talk to me via Empathy, and my Empathy chat window is 
closed, the message icon changes to color blue.
After opening the chat window, I don't receive notifications anymore. The 
message icon stay on it's default color.

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You received this bug notification because you are a member of Desktop
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https://bugs.launchpad.net/bugs/877698

Title:
  no notifications for direct IRC messages any more

Status in “empathy” package in Ubuntu:
  Confirmed

Bug description:
  No notification pops up any more since the update to Ubuntu 11.10 when
  someone mentions my nickname in an IRC channel.

  When switching back to the conversation windows the tab of the channel
  in which my nick name was mentioned is highlighted but no notification
  did pop up.

  Using Gnome Shell.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: empathy 3.2.0-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-12.20-generic-pae 3.0.4
  Uname: Linux 3.0.0-12-generic-pae i686
  ApportVersion: 1.23-0ubuntu3
  Architecture: i386
  Date: Tue Oct 18 21:37:23 2011
  EcryptfsInUse: Yes
  ExecutablePath: /usr/lib/empathy/empathy-chat
  InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release i386 (20101007)
  SourcePackage: empathy
  UpgradeStatus: Upgraded to oneiric on 2011-10-14 (4 days ago)

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