Mail messages arriving, then disappearing

I have Mountain Lion and the latest SpamSieve version. I’m having a problem where I see a new message come in via Apple’s Notification center, but then the message disappears from my inbox. Nowhere to be found in any of my folders. The odd thing is looking through SpamSieve’s log, there is a record of the message. This has happened on more than one occasion in the last day. Here is a part of the log for a message I saw come in, but then it isn’t in Mail:

Predicted: Good (1)
Subject: My resume
From: andrey@******.com
Identifier: Dl0sDjh0Wm/bYbBAFTvdkw==
Reason: (
“Andrey R”
) matched rule <From (name) Is Equal to “Andrey R”> in SpamSieve whitelist
Date: 2012-08-22 00:28:37 +0000

Help?

This log entry indicates that SpamSieve looked at the message but didn’t touch it. Perhaps you have another Mail rule that moved it, or it was moved by another computer or device. Have you tried searching for it with Spotlight or Webmail (if your server supports that)?

Sometimes re-building the Mailboxes helps !

Yes, the Mailbox > Rebuild command sometimes helps, as does rebuilding Apple Mail’s database.