AllowAnonymous not working with Custom AuthorizationAttribute

This has had me stumped for a while. None of the commonly encountered similar situations seem to apply here apparently. I've probably missed something obvious but I can't see it.

In my Mvc Web Application I use the Authorize and AllowAnonymous attributes in such a way that you have to explicitly open up an action as publicly available rather than lock down the secure areas of the site. I much prefer that approach. I cannot get the same behaviour in my WebAPI however.

I have written a custom Authorization Attribute that inherits from System.Web.Http.AuthorizeAttribute with the following:

[AttributeUsage(AttributeTargets.Class | AttributeTargets.Method, Inherited = true, AllowMultiple = true)]
public class MyAuthorizationAttribute : System.Web.Http.AuthorizeAttribute

I have this registered as a filter:

    public static void RegisterHttpFilters(HttpFilterCollection filters)
    {
        filters.Add(new MyAuthorizationAttribute());
    }

This all works as expected, actions are no longer available without credentials. The problem is that now the following method will not allow the AllowAnonymous attribute to do it's thing:

[System.Web.Http.AllowAnonymous]
public class HomeController : ApiController
{
    [GET("/"), System.Web.Http.HttpGet]
    public Link[] Index()
    {
        return new Link[] 
        { 
            new SelfLink(Request.RequestUri.AbsoluteUri, "api-root"),
            new Link(LinkRelConstants.AuthorizationEndpoint, "OAuth/Authorize/", "authenticate"),
            new Link(LinkRelConstants.AuthorizationTokenEndpoint , "OAuth/Tokens/", "auth-token-endpoint")
        };
    }
}

The most common scenario seems to be getting the two Authorize / AllowAnonymous attributes mixed up. System.Web.Mvc is for web apps and System.Web.Http is for WebAPI (as I understand it anyway).

Both of the Attributes I'm using are from the same