Settings don't stay set

The settings file is named prefs.js. The usual cause is being interrupted during shutdown by either an antivirus or VPN. Sometimes the file is read-only, in which case it's easy to fix. If you look in profile and see multiple prefs files, such as prefs-1.js, prefs-2.js, etc. that is further indication that thunderbird fails when shutting down. Although not a permanent fix, you can often restore the desired setting by removing all prefs files except the one with highest number, and renaming it to prefs.js. Repairing the cause is trial-and-error, again, usually an antivirus or VPN setting. That's all I know.