Why is my project still looking for Inject version 3.0.0.0

In the NinjectWebCommon.cs I have this:

private static IKernel CreateKernel()
{
    var kernel = new StandardKernel();
    try
    {
        kernel.Bind<Func<IKernel>>().ToMethod(ctx => () => new Bootstrapper().Kernel);
        kernel.Bind<IHttpModule>().To<HttpApplicationInitializationHttpModule>();

        RegisterServices(kernel);
        return kernel;
    }
    catch
    {
        kernel.Dispose();
        throw;
    }
}

When I run my ASP.NET MVC app it crashes on that method saying:

An exception of type 'System.IO.FileLoadException' occurred in Ninject.dll but was not handled in user code

Additional information: Could not load file or assembly 'System.Web.Mvc, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)

I have deleted my Ninject DLLs from the References and added them again from the NuGet manager and now my packages file looks like this, but still getting that error:

  <package id="Ninject" version="3.2.2.0" targetFramework="net451" />
  <package id="Ninject.MVC3" version="3.2.1.0" targetFramework="net451" />
  <package id="Ninject.Web.Common" version="3.2.3.0" targetFramework="net451" />
  <package id="Ninject.Web.Common.WebHost" version="3.2.3.0" targetFramework="net451" />

What else should I do?

If you want to easily figure out what project use what version, a solution is to go to the packages directory and look for the Ninject-[version] directory and delete, rename it or move it elsewhere. When you return to visual studio you should see what project is now complaining about not having it.