Thanks,
Decided to call CO and try and book something. DEN worked but GJT (grand junction) did not. The computer rejected it. All they could tell me was it was stating illegal routing. I suspect and the agent agrees that its because the route connects in DEN twice.
I am trying for IAH-SJO-IAH-DEN-GJT-DEN-EWR. The return is SJO to EWR with a stopover in GJT. Unfortunately there seems to be no way to avoid going via DEN both times and that I think is creating the illegal routing.