Did you use Vista's own Backup and Restore Centre?
If so, then here's a possible explanation of your problem (but I've never used this function in Vista, so I'm guessing).
If backing up your email data was simply a matter of ticking a box in the Vista Backup software, I wonder whether this does actually backup Outlook data.
Windows Mail is part of the Vista suite, but Outlook is not. So it's possible that just ticking a box within the Vista backup module would only backup data from Windows Mail.
As I said, that's just a theory from someone who doesn't really know what he's talking about. But if it's true, the I fear you may have lost your email data.