Yes, that is exactly it. arn made a change yesterday that caused older read threads to be marked as unread again. Just click Quick Links > Mark Forums Read.
Ok, I read the ENTIRE freaking thread (which started out talking about one thing and then switched to another...i.e. pointing out the change in the thread would be helpful since I don't read large or what appears to be irrelevant threads in their entirely as it takes too long).
In any case, that would explain the overall behavior (although I agree with the posters there that prefer a time-out since I don't like having to move to the end of 99 page threads just to mark them read when I don't care to read every message).
It doesn't appear to explain the other changes I believe I saw (some replies reappearing and others that came later disappearing as in the
Fully Functional MAME Emulator Appears in App Store, although I suppose I could be mistaking comments from another thread for that one. I'm pretty sure my comment about theft vs copyrights there was missing before and my reply to the last person in the thread about an alternative to iExplorer vanished the same time the other one returned.
Regardless, at least I know what the new setting is.