It is unread messages, not new messages.

But the very first thing is to disable all addons by restarting in Troubleshooting mode from the help menu to see if that is the cause, or there are issues with the graphics driver (unfortunately quite common on some distributions, depending on their stance on protected source). I am guessing the dark reader might well be the issue. But the results of the troubleshooting mode will be informative I think. No guessing then.

@Matt,

This morning I had nine messages on the main server, all unread, but a tag of 1 and only the newest message highlighted. On the second server a tag of 1 and one highlighted message. Tried the Troubleshooting mode. (Works nicely, very convenient!) It restarted with very different settings, but the exact same pattern of tags and highlights.

When I went back to my normal settings, it showed the same pattern again. But after maybe just enough time to check for new messages, the tag on the second server disappeared, and peeking at the inbox, that message was no longer highlighted.

I'd say the most typical behavior is that checking for new messages hides the highlights on all previously loaded messages, and marks the most recent of any new messages it finds with the highlight. But like in the screenshot I posted above, sometimes it does something randomly different.

For me it is clearly closer to "new messages" than "unread messages", but with a lot of mysterious randomness.

More screenshots of this and another problem...

Screenshot from 2024-01-17 12-40-56 TBird 1tag, no messages.png shows a tag of 1 on an inbox, but no messages at all. (But the top inbox is also sort-of highlighted, maybe it is confused?)

After clicking on the top inbox and back, there are four messages, the new one is not highlighted, one from last night is... /home/loren/Pictures/Screenshot from 2024-01-17 12-42-09 TBird peek other server, back, msgs.png

Seems random...