Since I upgraded to Windows 11, Thunderbird is (almost?) always preventing a clean Windows shutdown. It appears in the list of running programs which are shown after a few seconds, with the remark "this app is preventing Windows from shutting down" or similar. To me it looks as if it simply does not get or "listen" to the Windows equivalent of a SIGTERM on POSIX.
I can click "shutdown anyway", which supposedly sends the equivalent to a kill -9, apparently without harm; but I loathe doing that to a program handling essentially a user database.
This behavior was not there with Windows 10. It has, unfortunately, persisted through a few Windows and Thunderbird updates, which is why the exact versions are probably unimportant, but they are Windows 11 Pro 25H2 and Thunderbird 140.12.0esr (64-Bit), without any add-ons installed.
Otherwise, Thunderbird runs without issues. I can manually close it any time, and then Windows shuts down without major issues (one minor issue is that it sometimes waits for system processes like the Taskmanager to shut down, but they usually do a few seconds later).
My Google Fu betrayed me here, but I cannot be the only one having this issue.
Edit: When I tried shutting down with Thunderbird running in "Troubleshoot mode" as suggested in the deleted AI answer, Thunderbird (and then Windows) shut down correctly. Ever since, the issue has been fixed. The Thunderbird version did not change, and there was no major Windows update.