I am having trouble authenticating against the new REST Webservice API. We recently upgraded to version 3.5.3

Following is a code snipit.

msmProxyManager = new CounterSoft.Gemini.WebServices.ServiceManager("http://gemini", "", "", "", true);
try
{
    UserEN user = msmProxyManager.UsersService.WhoAmI();
    if (user.UserID > 0)
    {
        DialogResult = DialogResult.OK;
        Close();
        return;
    }
}
catch(Exception ex)
{
     MessageBox.Show(ex.Message);
}

We are now using windows authentication (a change we made when we upgraded).
I am getting a  "Method requires authentication" error on calling "WhoAmI". We have the anonymous user turned on in IIS. If this is turned off the "WhoAmI" returns an empty user (userID= -1), but we are also using the gemini scheduler and turning off anonymous access stops it from working.
Any one having this experience? How can I get the REST API to work with windows authentication?