You forgot to mention that in troubleshoot mode The default toolbar layout is used. See https://kb.mozillazine.org/Safe_Mode

   Safe Mode temporarily affects the following:

   • All extensions are disabled.
   • The default theme is used, without a persona.
   • The Just-in-time (JIT) JavaScript compiler is disabled.
   • The userChrome.css and userContent.css files are ignored.
   • The default toolbar layout is used.
   • Hardware acceleration is disabled.

That means that if e. g. you have activated the "Quick Filter" toolbar to display only unread messages and if you also activated the the pin icon "Keep filters applied when switching folders", you will only see unread messages in folders or none if they don't contain unread. (see picture) Now when you start TB in troubleshoot mode your filters will be disabled and you can see ALL your messages again.

Thanks for that suggestion, but I haven't actually been using the "quick filter" feature. In fact I couldn't see your message in Thunderbird, only when I log on to the fastmail server. And Thunderbird does show me some of the messages which I have already read; reading a message doesn't seem to affect its visibility.

For some senders I get all messages, for some none (they appear only on the server). So far I have found no senders for whom some messages appear and others don't. It seems that Thunderbird displays only messages from senders who are in my address book. Might there be a setting somewhere to fix this?

You also note that troubleshooting mode uses the default theme. Looking at themes, I am using the system theme labeled as "auto." "Light" and "dark" themes are also offered, and I tried each with no effect on which messages are visible. As for the other items --

  • The Just-in-time (JIT) JavaScript compiler is disabled.
  • The userChrome.css and userContent.css files are ignored.
  • The default toolbar layout is used. --

I do not know how to set the first two, and would appreciate knowing how to verify that the the "default toolbar layout" is what I am using now. Thanks again for taking the time to look at this.

SOLVED! This problem is addressed at https://support.mozilla.org/en-US/questions/1502925 It does seem like a suboptimal user interface, that the user can so easily do this unintentionally.

1. You can't manually enable/disable JIT 2. If you haven't created userChrome/userContent.css, you don't have them anyway 3. The default toolbar has nothing on it except a very large search box at the top of the page 4. There is no specific setting in Thunderbird for displaying only messages from senders who are in your address book. One way to accomplish it would be with filters. Have you made any?

For some senders I get all messages, for some none (they appear only on the server). So far I have found no senders for whom some messages appear and others don't. It seems that Thunderbird displays only messages from senders who are in my address book. Might there be a setting somewhere to fix this?

Your problem can be explained by an activation of the button "Show only messages from people in your address book" in the "Quick Filter" toolbar (see my picture)

SOLVED! This problem is addressed at https://support.mozilla.org/en-US/questions/1502925 It does seem like a suboptimal user interface, that the user can so easily do this unintentionally.

You may have noticed that the solution in the linked question is MY solution. And yes, many people activate this Quick filter toolbar unintentionally which means that the UI is suboptimal ....

Thanks. I will update the related KB articles