Microsoft has released the second cumulative update for System Center 2012 Configuration Manager SP1.
The Installation process from the CU2 was changed a Little bit, and more Linux distributions are now supported by SCCM:
http://blogs.technet.com/b/configmgrteam/archive/2013/06/21/now-available-cumulative-update-2-for-system-center-2012-configuration-manager-service-pack-1.aspx

See the blog post from Ronni Pedersen about installing CU2:
http://www.ronnipedersen.com/2013/06/installing-sccm-2012-sp1-cu2-quick-start-guide/