Here is the example I had, but the situation no longer exists.
The international flight arrives in Houston at about 11am.
Possible connecting flights to San Diego are at 12:35, 2:18, 6:00, and 9:15 pm.
The total fare if I took the 6pm and 9:15 pm flights was $691+. The fare if I took the 12:35 and 2:18 flights was $764. No big deal. Then I punched up the r/t fares from SAN to IAH on the same dates, and the fares were $243 on all four of the flights. (ie no price difference) So, I could not see why there should be a $73 price difference with taking the later, as opposed to the earlier flights.