first of all, I have a .NET 4.0 application with this configuration:
When I ran into this problem, the reason un-checking the schema didn't take turned out to be having multiple instances of Visual Studio open.
(I had VS2015 open with one project and VS2013 also open at the same time with a different project.)
Note, multiple versions of Visual Studio and switching back and forth on the same project/solution also seems to be how some issues with repeated schemas occurred in the first place.