Because of troubles with the debug software I updated my MPSS version with the hope, that this will resolve (some) problems. So I downloaded my the latest version from http://software.intel.com/en-us/articles/intel-manycore-platform-software-stack-mpss and followed my own tutorial from [1]. The only thing, that you have to change is the spec-file, if you want the Intel tools to show you the correct version of it. The appropriate file can be downloaded here: intel-mic-kmod-5889-16.

I did a complete uninstall of the previous version and after a restart I installed the newer one. Everything runs like before. Not worse, but still not better…

Sources:
http://www.theismus.de/HPCBlog/?p=1