Ok.. Here's my take.
You open raise from MP with ATo.
Flop comes JQQ. He checks, you bet, he calls.
If he has something (Qx (which he did), or Jebus-forbid QJ) and he bets the flop, he may chase you out if you think you're in trouble. His check says, "I don't have anything, but I want to see the next card for a small bet." That's what he WANTS you to think. The
![The Three of Hearts [3h]](https://pofex.com/images/smilies/3h.gif)
on the turn puts a flush draw on the board. Follow my logic. He's thinking of what you would raise with, and what could put him in trouble:
"Underpair, AK, AT, other suited paint?"
The second heart (I assume the flop was a rainbow) could give you a flush draw with Axs (hearts), so his trip queens become vulnerable. He was slowplaying them, hoping for a crappy turn card. Your raise, his reraise and your call just fluffed the pot for him. He knew he had the best hand when you raised him, but he wanted to make you pay to see the river and your possible flush. When you didn't re-raise him, he figured you didn't have AQ, so the ace on the river basically left him thinking that only AA has him beat, especially since you won't open raise from MP with KT. He was worried about the straight, the flush, and when neither came, he knew he had you.
Basically, he slowplayed his set. The heart on the turn scared the hell out of him, and woke him up--plus he knew he couldn't make up a bet on the river, especially letting you draw to either a straight or a flush.