Do you mean that there are two backups from different computers (or a second backup for one PC) on the external drive? When an external drive is used for backup, each computer gets its own folder. It gets a new folder on a reinstall or a new/complete backup.
You should be able to select a custom backup to see the backup seletions. If you desire, you can also open the backup .zip files manually using WinZip or other 3rd party tool.
If you need help, please open a support case.
How to reach support (FAQ) -
http://social.microsoft.com/Forums/en-US/onecareinstallandactivate/thread/30400b52-7f26-4ba0-bc18-17e305329d90
~ Microsoft MVP Windows Live ~ Windows Live OneCare| Live Mesh|MS Security Essentials Forums Moderator ~