This is how we override the OwinMiddleware...first we created our own middleware on top of Owin...I think we had similar issue as you did.
First need to create a constant:
public class Constants
{
    public const string OwinChallengeFlag = "X-Challenge";
}
And we override the OwinMiddleware
public class AuthenticationMiddleware : OwinMiddleware
{
    public AuthenticationMiddleware(OwinMiddleware next) : base(next) { }
    public override async Task Invoke(IOwinContext context)
    {
        await Next.Invoke(context);
        if (context.Response.StatusCode == 400 && context.Response.Headers.ContainsKey(Constants.OwinChallengeFlag))
        {
            var headerValues = context.Response.Headers.GetValues(Constants.OwinChallengeFlag);
            context.Response.StatusCode = Convert.ToInt16(headerValues.FirstOrDefault());
            context.Response.Headers.Remove(Constants.OwinChallengeFlag);
        }
    }
}
In the startup.Auth file, we allowed the overrid of the Invoke Owin Commands
public void ConfigureAuth(IAppBuilder app)
    ....
        app.Use<AuthenticationMiddleware>(); //Allows override of Invoke OWIN commands
    ....
    }
And in the ApplicationOAuthProvider, we modified the GrantResourceOwnerCredentials.
public override async Task GrantResourceOwnerCredentials(OAuthGrantResourceOwnerCredentialsContext context)
    {
        using (UserManager<IdentityUser> userManager = _userManagerFactory())
        {
            IdentityUser user = await userManager.FindAsync(context.UserName, context.Password);
            if (user == null)
            {
                context.SetError("invalid_grant", "The user name or password is incorrect.");
                context.Response.Headers.Add(Constants.OwinChallengeFlag, new[] { ((int)HttpStatusCode.Unauthorized).ToString() }); //Little trick to get this to throw 401, refer to AuthenticationMiddleware for more
                //return;
            }
            ....