Well, if there are 2 double cert combos, the system has to pick one.
I did a little testing, I think the order of priority is:
Special 2 Cert Combos > STR > AGI> LCK> WIS>INT
I tested with a couple special double cert combos, it appears to work in the same order.(Def>Melee>Range>Healing>Magic), which is the same order as the list of classes in the class changing window.