DPM is great for backing up SharePoint data, but when you select to back up the SharePoint role of a server, DPM will only backup the SharePoint_Config database and the content databases, which is less than ideal.
To back up the SharePoint Server properly in DPM:
Figure: Notice that SharePoint protection only selects the SharePoint_Config and Content databases
Figure: Ensure you back up the remaining databases in the SharePoint SQL Instance
After following these steps you will have full protection of your SharePoint databases.