Unread Mail badges won't go away

Mail v7 (1822). Anyone else have this issue? I have many folders set up within Mail. I have an IMAP account, but have Rules to transfer messages to folder On My Mac. What's started to happen is the badges that usually appear associated with the folder where the new, unread message has been moved, will not go away after the message is read.
Obvioulsy the result are a lot of badges on folders that contain all messages that have been read. The only way to fix this is the quit and restart Mail. Any thoughts, or anyone else with this problem?

I've been experiencing this on laptop running Windows 7.  Prior to a few months ago, I did not have any issues with this.  Skype version is the latest (6.11.0.102).  If I have multiple messages from same contact, I can get all but one notificationto go away for that contact by marking as read.  But I can't get the last one to go away.  Restarting Skype doesn't work, and rebooting laptop doesn't work.  It does eventually clear (in a day or two) but very frustrating until it does.  And it is random - doesn't happen all the time, and doesn't seem to happen on group messages.  If it is contact-specific, it is more than one contact that has issue.
Does anyone have any ideas?

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