You may need to re-download Configuration Manager 2012 and Endpoint Protection 2012 SP1 Binaries!
The binaries for System Center Configuration Manager 2012 and System Center Endpoint Protection 2012 have been updated to correct some minor issues. The binaries have been updated at the Download Center, and also on the Technet and MSDN download sites. For Configuration Manager 2012 SP1, the updated download release of SP1 includes the following hotfix: Installation error 0x800b0101: System Center 2012 Configuration Manager Service Pack 1 client
For Endpoint Protection, the new binaries include fixed files (Linux/iOS) that were corrupt in the initial release. This means if you downloaded the binaries prior to today (25/01/2013) - you will likely need to re-download them