Steps

1. In the messages listing pane, activate "Display message threads"
2. Activate "Sort by read"

Expected

All unread messages appear at the top of the list, including threads with unread first or subsequent messages.

Actual

All unread messages, which are not part of a thread as well as threads with the first message marked unread appear at the top of the list, sorted also by date with the newest first. Then read messages and threads follow, newest first.
Threads with any subsequent messages being marked unread are still sorted as part of the "read messages" list, therefore harder to find / easy to loose track off.

I don't think exactly this has been raised yet here: https://bugzilla.mozilla.org/buglist.cgi?quicksearch=thread%20order%20by%20read&list_id=15804071

Happens in safe mode?
https://support.mozilla.org/en-US/kb/safe-mode-thunderbird

Yeap, the same in safe mode.

Tested with a thread of three emails, all from the same day. Marking the initial one as unread and resorting "by read" move the thread into the list of unread messages at the top.
Marking only any of the subsequent ones as unread keeps the thread listed within the "read" messages, sorted only by the initial message's date.

Wayne, I don't think this is new btw. Pretty sure 78 was the same and maybe all versions before. I keep changing how I sort, maybe that's why I didn't see it before, or simply because I didn't know about the messages I missed ;)

This bug is new in V91? Given sort by is set to threaded, I would have assumed that would be the expected result, as sort by would take precedence.