Do you use a computer file cleaning product like CCleaner or even some AV products can clean up files? If yes, recommend you do not allow it to have any access to any Thunderbird file or folder. They have a habit of removing/cleaning up temp files, session files, password files etc and can cause odd anomalies. If you set up to show or not show unread, then it will be remembered in session files etc. If a product cleans up files with preferences remembered then Thunderbird will not know about them when it next runs.

This could explain why it works intermitantly.