I had the same problem as a lot of people here i.e. not being able to backup all my mails which are in Thunderbird. The mails are stored in file with no extension. The .msf that Smartware are copying are useless, they do not contain the mail but are only some indexes…
So the main thing to know is that the rules are stored in a file named Backuprules.xml on your computer (on Vista : C:\Users<your login>\AppData\Roaming\Western Digital\WD SmartWare).
You can edit this file and modify the rules in there.
For instance, for Thunderbird, I replaced the following rule
Et voila ! My whole thunderbird profile is now stored automatically and categorized in the MAIL repository.
The category of data is coded in the key “ProviderID”. Thus you can easily find which rule belongs to which category of data.
Good luck !