Moving a message to a folder corrupts the folder

Any time I move a message from one folder to another, the destination folder apparently becomes corrupted. I say this because I can "repair" the folder and that works - until I move another message into it.
Symptoms: I can see the message header in the message list pane, but cannot see any content in the message pane, nor does any content appear if I open the message in a tab. Sometimes repairing the folder once brings the message back, but the view is raw data (with header information and html tags); in this case, repairing it a second time fixes that problem. The message does automatically show as "read" after the requisite time period. Compacting the folder has resulted in the loss of the message completely (though only from the folder; it was still in the archive).
I have deleted the global-messages-db.sqlite file and recreated the index - no change.
Running Thunderbird 24.5.0 on Ubuntu 12.04.4, 3.2.0-64-generic kernel. My main e-mail source is an imap account. Apparently the problem does not exist when receiving mail in a pop account (at least I haven't been able to recreate it with minimal testing).
Any help would be very much appreciated.

So... i can NOT move a message (received via IMAP) to a folder without corrupting the folder (sometimes I can see the message header, sometimes not, but the message body comes up blank). So before moving a message to a folder I have to "repair" the folder, then move the message, then "repair" the folder again. Having to do that for any and every e-mail message I want to save is becoming... tedious.
One suggestion was to compact the folders; that happens automatically. Just to be sure, I've compacted a folder and then moved a message in - same problem.
Another was to make the folders smaller, so I moved a lot of messages (literally thousands, bordering on ten thousand or more) to the "Local Folders" section - no help there either.
The article in the answer from finitarry suggested using a tool to break the folder into 500 message chunks (so I could look for the corruption). Perhaps I misread the article, but it seemed to be looking for the raw files - hence my listing of the file structure for my profile. I have no idea which one to use for that. Editing text files - not a problem, and I do have an editor that will handle large files (vim).
If there is a way to export everything (and keep the folder structure) I can move all of the messages to Local Folders, export, and then import (assuming there is a chance that would fix things).

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