In July 2013 Microsoft noted that the Update Rollup 3 for Data Protection Manager 2012 SP1 released with issues. Go figure, huh? With the number of botched updates recently (and over the previous months), this seems to be sort of commonplace.
After identifying the issues, Microsoft provided workarounds which included running a SQL script against the DPM database.
The two issues (with workarounds) are documented here: Important Update on DPM 2012 SP1 Update Rollup 3–Issues and Workarounds
For those that were afraid to install UR3 after the issues had surfaced, Microsoft has now released a UR3 version which includes the fixes.
The System Center 2012 SP1 UR3 package for DPM was re-released on 8-20-13 and fixes the above two issues. You can simply install the new UR3 re-released package available here:
KB2877075 - Rollup 3 for System Center 2012 SP1 - Data Protection Manager (http://catalog.update.microsoft.com/v7/site/Search.aspx?q=2877075)
The new DPM version will be 4.1.3417.0 after applying this update.