Hello,
I noticed that after an windows update my linked clones are exhibiting a high CPU activity. It turns out that after a.NET update windows is re-compiling .NET assemblies in the idle time. Not good if you have a hundred of VM doing this. A workaround is to force the rebuild to happen before you clone the base image:
x64
%windir%\microsoft.net\framework64\v4.0.30319\ngen.exe update /force
x86
%windir%\microsoft.net\framework\v4.0.30319\ngen.exe update /force