Ok, i’ve got it.
The Problem is, that my systems a 64 Bit systems and the aspnet_regiis i’ve called was the 32 Bit Version. After calling aspnet_regiis from the Framework64 Directory everything was fine.
Thanks to Scott Hanselman http://www.hanselman.com/blog/ASPNET4BreakingChangesAndStuffToBeAwareOf.aspx