If this is for pathfinder 1E, it isn't taking the lower one, it is taking the first one. It will always roll twice for each attack, because it rolls the attack as well as the critical confirm roll in case the attack is a critical threat. The roll template (html/css) is set up to hide the critical confirm roll in chat unless the first roll is a critical threat. It is doing the same thing with damage. It will roll regular and critical damage all at once. The roll template will hide the critical damage unless the attack roll was a critical threat. 3D dice will render the roll of all dice used, so they always show all the dice rolled.
