Thunderbird does not always highlight folders with new unread messages despite receiving them.
I have been having an issue with TB not highlighting (aka changing folder name font to bold and showing number of unread messages inside beside it) some folders which have received new messages. The folders appear as if nothing has been received. The new messages are in fact inside after I open the folders but they are already marked as read despite me never actually reading them or even opening the folder. Restarting TB or PC or downloading mails does not fix it. It is possible to be completely unaware of a new mail until I manually check every folder for those "ghost messages".
To be clear I do have all the 3 options of checking for new mails turned on on every adress added in TB.
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same email address configured say on your phone. IF they are read there, or in some cases downloaded to a POP mail client than they are shown as read on the server and as such are not "new" as far as Thunderbird is concerned. Being marked as read is often a clue the issue is related to synchronization of status for another device.