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Why does Thunderbird open two separate windows, if I close one, both shut down.

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As in description. When I start Thunderbird it starts two separate windows. If I close one, the other one also closes. It’s possible to work in both windows, but they don’t sync until restarted.

As in description. When I start Thunderbird it starts two separate windows. If I close one, the other one also closes. It’s possible to work in both windows, but they don’t sync until restarted.

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Are you using the MinimizeToTray add-on, or a similar one?

If so, disable it, restart Thunderbird like you normally do, and re-enble it if all goes well. You should also temporarily start Thunderbird in Safe Mode to see if any other add-on is causing the issue. In that mode, Thunderbird should work as expected. Note that the original MinmizeToTray add-on is rather outdated, so if you can pinpoint the issue to that add-on, you could try finding a replacement.

In general, this should solve it too:

  1. Go to File > Close (NOT Quit, but Close), that closes the window.
  2. With the last window, quit.
  3. Open Thunderbird. There should be only one window, as expected.

See this bug for more info. Please don’t comment there but read the last comment with care.

Does this help?