First, due diligence: are you sure you're actually running 64-bit? By default new projects get that dumb "Prefer 32-bit" option checked, so an AnyCPU build will still run using 32-bit. Also, make sure if you've got the debugger attached that you don't have it set to inhibit optimizations. By default most optimizations are disabled even in release mode when a debugger is present, for obvious reasons.
Also, be careful about which package you're using. The JIT looks for a very particular assembly to enable intrinsics, so if there is a mismatch in which build you're using it will just not optimize it. Doesn't .NET 4.6 ship with an older System.Numerics.Vectors assembly built in, or is it still recommended to grab one from NuGet?