Mail has collapsed: No Content - Emergency

I am reposting this question, becuse I mistakenly marked it as solved. It is far from solved. Mail keeps losing its content. I have reindexed mailboxes, and the content comes back, but the slightest action in Mail, like trashing one email, and it all vanishes again. I was going to try to rebuild the mailboxes immediately after reindexing them, but the last time Mail came up after reindexing, the first click produced the Spinning Beachball of Death. It lasted a couple of minutes. Then I was able to rebuild all mailboxes. It looked like everything was fixed, but then I quit Mail & restared it. Everything gone again!
This is ridiculous. Mail has collapsed. Reindexing and rebuilding do not stick. The problem repeats itself. I clean installed my Mountain Lion system to avoid stuff like this. What is going on?

Booted from another drive & ran Disk Warrior. Directory was 41% out of order. I have never seen a directory this scrambled. Repaired directory. Rebooted into my main system, and reindexed mail. Mail started up to a blank state, and Activity Monitor shows system processes mds, mdworker, etc, working overtime.
Mail has no content and its Trash box is missing.  I am going to restore the entire user Library-->Mail folder from Time Machine to see if it helps. No other problems on the computer. This seems to be just about Mail.

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