After installing SP1 to SQL Server 2012 (11.0.3000) on one of our servers, I noticed higher than normal CPU loads due to msiexec.exe running non-stop. The cpu percentage would bounce from 0% to 13%, and the application log would have five new entries about MsiInstaller and RestartManager about every 30 seconds. There is a Connect bug about it at msiexec.exe processes keep running after installation of SQL Server 2012 SP1, and a fix has just been released at Non Security Update for SQL Server 2012 SP1 (KB2793634).
After installing the fix, SQL Server will be at version 11.0.3128, you will no longer see msiexec.exe running, those log entries will stop, and your CPU usage will drop.
SQL Server 2012 SP1 – Endless MsiInstaller Application Log Entries