We're using the Small Business Server Backup that comes with SBS 2008 to backup all drives to an iomega iSCSI-Target. The Backup works fine and everything is shown as successfully backed up.
But the exchange-logs in C:\Program Files\Microsoft\Exchange Server\Mailbox\First Storage Group
and C:\Program Files\Microsoft\Exchange Server\Mailbox\Second Storage Group
aren't flushed.
What could cause this behaviour?
When you look at the backup configuration, is the box to backup the Exchange Information Store checked, or are you only backing up the drives?
Here is a link that can do what you need on Win2k8 R2, I know you are referring to SBS however not sure how many features are included for 'Window Server Backup' within SBS.
In summary: Windows server backup->Backup schedule->Modify Backup->Custom->Add items + Advanced Settings=>Vss Settings=>VSS FULL BACKUP->Backup Time->Destination Type->Keep or Change Backup Destination->Finish [Verify that in advance option you see VSS full backup]