Help with missing folders in Leopard Mail

Since upgrading to MobileMe, I have had some problems with Mail deleting my custom folders. Prior to MobileMe, I had several folders with hundreds of saved messages. Now, however they are gone. I have 5 different computers that used to have the folders on them and now 4 of them have had the folders deleted.

When I first noticed the folders missing on my main computer at home I thought that it was a temporary problem with MobileMe and that they would reappear. However, I went to work and checked my 2 computers there and they also were missing. So, when I got home I pulled out my trusty Powerbook G4 to verify. When I first opened Mail the folders were there (remember it is slow), but as Mail synced with MobileMe and imported the new mail the folders disappeared right before my eyes.

Now, I have one computer at home that I have taken offline because it still has the folders on it. Anyone have a clue why this is happening. I thought that any folders on my computers at home and work would have their mail and folders synced to MobileMe. Or, am I wrong?

I have checked in user/lib/mail/....... for the folders but they are not there. Is there any way to recover the missing messages?