Some read mail items remain marked as unread

Some read mail items remain marked as unread (even after I've read them).
I have to manually mark them as read.
This doesn't happen to all mail items, just some.
How can I fix this?

A few discoveries I made this morning.
One is that disabling GPGMail seems to solve the problem, or at least significantly reduce its occurrence.
Another is that with GPGMail enabled, it seems to depend on how quickly one opens an email. I can't say for sure that this is a hard and fast rule, but messages staying unread seems to be more of a problem if you've just entered the folder or just been viewing another message and suddenly change to an unread one. It's as though GPGMail causes Mail to need some time to think things through.
A third is that if you have multiple mail accounts, a workaround to reset the unread count exists. If a mail folder in Account One is having problems, you can switch to a folder in Account Two, possibly wait an interval of time (not sure what that interval would be), then switch back to your original Account One folder. That seems to force a refresh of the unread count, without needing a folder rebuild (with consequent loss of expanded threads, etc).
However, for the time being, I've just disabled GPGMail. I can re-enable it as needed, by the looks of it, and it's not as though I've really needed to use it yet.
I could wish, though, that Apple offered proper GPG support, or at least that they made enough of their API available that third parties could do a proper job instead of an ugly and somewhat broken hack. (I've also seen complaints that Apple like to change their API without telling anyone, just to keep third-party developers on their toes =P.) I suppose another problem is lack of available time. Which I also suffer from, so I don't think a "real solution" is forthcoming from this quarter, at least.

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