Looking at this thread again, I realize that I've never had to reselect not to show already known abilities. Looking in my WTF folder, Blizzard saved your selection to a saved variables file, so that it is remembered between sessions and applied account-wide. Mine says:
Code:
TRAINER_FILTER_AVAILABLE = 1
TRAINER_FILTER_UNAVAILABLE = 1
TRAINER_FILTER_USED = 0
Are you certain that you don't have anything else interfering with this function? Do you get the same behavior with all addons disabled?