I always thought the "direct" flights between IAH & MAD were in anticipation of non-stop service. Even though Continental management at the DO's has indicted that the non-stop service is high on their list, the entry difficulties for non-citizens who might just transit IAH to MAD and lack of sufficient widebody aircraft has put off a non-stop indefinitely, AFAIK.
Two years ago we returned in BF on Flt. 63 which also arrived late and a concierage was waiting for us to advise we were seated up front on the next later scheduled flight EWR-IAH.