Ended on a hand of: K J A A Q and did not receive the Jacks or Better $1 payout. According to a brief search about the rules of video poker, a pair of aces is considered better than a pair of jacks.
It's different on or before the second deal?
Aces _can_ be low in the case of an A-1-2-3-4 straight, but they can almost always be high as well, and almost always beat K.
Having aces always be low/never be high is super uncommon (it may not even exist in Poker, but I can't say for certain).