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It seems that the version "pine-4.20-2.i386.rpm" doesn't unset the unseen flag on messages properly. When I have a new messae in a folder or system-inbox and I read it, it should reset that flag to seen. But when I quit pine and re-enter pine again that message is sowing up as unseen. The same symptom is also occuring when I read unseen msg's and return to pine after quiting. The last version didn't had that problem... I don't recall If I upgraded from 4.10-x or 4.20-1 ...
Have you checked that you don't have a stale lock file floating around somewhere? I had this very problem a while back, and it proved to be because netlag had killed my telnet, causing pine to abort abnormally, and when I next connected and ran pine, the stale lock flag resulting from the crash held the PID of another user's pine process, causing pine to go into READ-ONLY mode. I don't know whether the fact that the PID had been reused was relevant, but certainly the behaviour was there...
No I don't think it has to do with a lock file because then you will be warned that pine is in READ-ONLY mode. Because I don't get that kind of message or indication I don't think that's the case. Furthermore it happens in ALL folders so...
This seems to be fixed in the ones included in Red Hat Linux 6.2