This ability to use A-B-C bookings for lower fares comes and goes on southwest.com. Old-timers will recall the intense interest in being able to force the website to display the full fare matrix specifically for purposes of finding combinable fare classes that would produce lower fares on connecting flights. (Relative n00bs can search the forum archives for insight.)

As to the specific situation, I can't give an explanation, other than to say that WN's fare coding is complex and proprietary. End result: weird stuff happens.