I just had the above mentioned thread stuck unread again and there was
only one other thread unread in the subforum. I just read the other unread thread and after that also the stuck unread thread was marked read!
Initial note: I have resisted the temptation to use the workaround of just marking an entire forum as read, until this very moment. For the sake of the discussion, I have chosen to abandon that preference, at least temporarily. It has been somewhat illuminating, I think. Having said that, here are some additional observations, along with some theories:
As you (and others) have noted, if you mark an entire forum as read and one of the affected threads is in that forum, the thread will indeed "lose" the glitched state and be marked correctly on the Watched threads page -- at least temporarily. I believe we can reasonably hypothesize that the glitched thread will present the appearance of normal behavior until another thread in that forum receives a new post -- however, this hypothesis seems to be incomplete; this only appears to be the case when the affected thread is listed on the
first page of posts for that forum, consisting of the most recent fifty threads in that forum. If the thread falls dormant for long enough that it ends up beyond that first page, it appears that it can remain un-glitched until another unread message reaches the same page that has the glitched thread on it. (In some cases, this may not even be possible for a "fully read" forum, given that there are likely to be other dormant threads between the glitched thread and the most recent unread thread.)
Caveat: If a thread has been pinned, it seems that it can present the appearance of being un-glitched, even with new posts in threads within that forum -- however, I suspect that this reprieve may be lost when another pinned thread in that forum receives a new post.
These observations and theories are based upon my own experience with three threads in the iPhone forum and the News Discussions forum. One of my affected threads is the pinned iPhone cases thread in the iPhone forum, and two other affected threads were in the News forum. Since marking these two forums fully read while typing up this post, at least ten News threads have received new posts, but neither of those affected threads in News appear on the first page, and so they have not returned to a glitched state -- yet. Likewise for the iPhone cases thread; it remains un-glitched for now, but there are not yet any new posts in the other pinned threads; only in a few of the regular forum threads.