I finally solved a mistery which was bothering me for months. #Thunderbird was flagging most but not all messages in one of my mailboxes as important. I could not find any setting or rule in Thunderbird responsible for this behavior. Finally I found the root cause which was the #Nextcloud Webmail App which I have configured but rarely use. 🙈
https://support.mozilla.org/bm/questions/1345280