Backup file types
The types of files that Windows Live OneCare version 2.0 can back up has changed since version 1.6. OneCare won't back up any files that are located in the Windows folder or the Program Files folder. In addition, version 2.0 can no longer back up the following file types:
The size difference is most certainly due to the inclusion of any of the above file types in your \My Documents folder plus (more likely) the compression used by OneCare backup.
-steve