I think it returns to default (adjusting the keyboard light based on ambient light) after you wake it from sleep or reset it in the system prefs. On mine I don't really pay attention to the keyboard light, but it seems to be on when I need it and off when I don't.
Im not really sure of your circumstances, but I assume you're saying when you override the automatic setting with the F keys, then turn automatic back on in System prefs, the KB light doesn't turn back on. Try taking it to a dark room and see what happens, or put it to sleep then wake it up