I'm not sure what the standard raise is on Poker Stars, but I struggle to put the villian on KK -> JJ as a 3xBB raise, sometimes isn't enough to get donks out with an A, rag - depending on how he has played in the past 80 hands he could be sat there with A, rag suited, so could quite easily be 3oak by the turn.
If I was in his position, I'd put you on A,x and then I'd have to weigh up the odds
of it being A,Q. What would his read be on you? I'd be inclined to think, as you have position, you were just trying to buy a free card on the turn and were drawing to something (possibly the flush or over pair) so he has tried to catch you out. One thing I do know is that he doesn't want you to see the last card, which would indicate his hand is completely ruined by a flush, so we can rule out him having 4oak, FH or anywhere near the nut flush. If he had a 5, he would not re-raise on the flop, so we can confidently rule out 3oak, so I'd put him on a mid range PP (10->6) or a weak draw. Depending on what my roll was like, I'd call as I'm 80% sure he needs to catch on the river to win. The 20% doubt is that he's got A,A and played it cleverly by not re-reraising preflop.
Edit: Sorry, just seen your villian stats at the top and that you had the Ah!