Well, glad you have clarity. Mentioning you had made a multi-city booking would have been useful to those trying to provide focussed comments. The multi-city tool is indeed the low point of the booking engine, especially as it defaults to the lowest possible fare class.

For what it is worth, sometimes I book the domestic Thailand sectors separately as the price overall can be cheaper and avoids having to use the (very poor) multi-city tool. Sometimes, however, THAI has fares where a domestic destination other than Bangkok has very good pricing, and then things do become tricky if you want a better fare class than it comes up with - say for miles or luggage.