There are lots of setting over at LHC you obviously did not understand.
Hence, your ATLAS native tasks are completely misconfigured.
The major issue is that you force a 12-core setup on a 12-core CPU.
This collides with your BOINC setting where you try to reduce the #cores.

As a result other tasks - especially the GPU tasks - and the OS don't get enough CPU cycles to work fine.

You should ask at the LHC@home mb how to correctly set up ATLAS native.