Microsoft released RU3 for DPM 2012 SP1. Finally I was able to upgrade the DPM Agent on SharePoint 2013 as I kept getting an error when trying to Protect SQL.

The updated agent installed fine, first initial sync when perfect until it finished with the above error.

Here are the steps I did to fix it:

• Reran ConfigureSharePoint.exe -EnableSharePointProtection and entered the same account as the Farm account in SharePoint.
• “c:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\15\BIN\stsadm” -o registerwsswriter (run this from an elevated prompt)

hope it helps