Confirmed that this same behavior occures in 12.04 LTS. The following
behavior has been observed:

After login, open thunderbird. After some period of usage, thunderbird
will no longer appear in the alt-tab window switcher. In order to get
the icon to re-appear you must run "unity --replace", as stated above.
Since having found the above work around I've yet to have the icon
disappear on me again (roughtly 30 minutes). If I can come up with any
repoducable steps I will post and update.

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https://bugs.launchpad.net/bugs/865302

Title:
  Unity thunderbird integration broken

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