I overrided the isUserInRole function of 
org.jboss.portal.portlet.impl.spi.AbstractSecurityContext, like this to solve 
getting the user roles from the SecurityAssociation (whose subject i set in the 
filter) and instead from the request object.
   
  |    public boolean isUserInRole(String roleName)
  |    {
  |      if(SecurityAssociation.getSubject() != null
  |           && req.getAuthType().equals("NTLM"))
  |      {
  |          boolean inRole = false;
  |          Object[] principals = 
SecurityAssociation.getSubject().getPrincipals(SimpleGroup.class).toArray();
  |          
  |          SimpleGroup roleGroup = null;
  |          for(int i=0; i<principals.length; i++)
  |          {
  |              SimpleGroup temp = (SimpleGroup)principals[ i]; 
  |              if(temp.getName().equals("Roles"))
  |                  roleGroup = temp;
  |          }
  |          
  |          if(roleGroup != null && roleGroup.isMember(new 
UserPrincipal(roleName)))
  |             inRole = true;         
  | 
  |          return inRole;
  |      }
  |      else
  |          return req.isUserInRole(roleName);
  |    }
  | 

I have commented out all the security constraints, and the security-role-ref 
from the servlet definitions in web.xml

It worked all well. But is it the right way to go about ?

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