When creating the backup job for Exchange 2007 you will NOT see individual mailboxes. You will only see the Information Stores. After the backup has completed of the Exchange Information Stores, check your restore selections and you should be able to drill down to individual mailboxes and items. If you can't, check the backup job properties in the Exchange section and make sure the check box for Granual Restore Technology is checked.
If the backup was successful you should be able to drill down to mailboxes, if not I would strongly suggest giving a call into support to have them debug the backup to find out why it's not showing the mailboxes.
If the backup is failing, what is the error in the backup job?
Also make sure you have SP2 installed on the media server and you updated the remote agent after installing SP2.