Mail tagged as "not junk" is hidden and produces console error

Mail has developed a strange quirk since the latest OS update. Can anyone help me fix it?
Whenever I un-mark email that was automatically marked as junk, the messages become hidden in the inbox. By "hidden" I mean that the next time I run mail, there is a gap in the inbox list where the message used to be -- almost as if the time/subject/etc. were all written in white font. Clicking on the gap opens the message, and clicking "Junk" then "not Junk" restores everything to normal... until the next time I open the Mail program.
Note that this seems to happen both to my dot mac e-mail address as well as to a third-party IMAP account.
I've also begun to see odd messages on the console, like:
Server sent warning response for command APPEND: * NO Unknown flag: NotJunk
and
Server sent warning response for command APPEND: * NO Unknown flag: $NotJunk
My guess is that Mail is trying to add some sort of (unsupported?) tag to messages which is causing problems. Is there any fix? Alternatively, is there any way to get it to stop automatically marking mail as junk?
Thanks,
Mike

Hi zengo giri, and a warm welcome to the forums!
Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup), it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, then move these folder & file to the Desktop.
Move this Folder to the Desktop...
/Users/YourUserName/Library/Caches/Mail/
Move this file to the Desktop...
/Users/YourUserName/Library/Mail/Envelope Index
Reboot.
If that doesn't do it try these & reboot...
/Users/YourUserName/Library/Mail/MessageRules.plist
/Users/YourUserName/Library/Mail/MessageRules.plist.backup

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Mail tagged as "not junk" is hidden and produces console error

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