I have a similar issue in that after loading MiniProfiler and MiniProfiler.EnitiyFramework6 I have this issue. MiniProfiler runs fine, but when I add to my Applcation_Start
Turns out that this may be related to versions and ids. If you install MiniProfiler.EntityFramework6 without installing the other packages, nuget will handle the dependencies, but it puts the wrong #s in the web.config here (make sure the version number is correct):
If you uninstall all the MiniProfiler packages and then install in this order:
MiniProfiler
MiniProfiler.MVC4
MiniProfiler.EF6
It seems to work ok.