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I guess my dilemma is that KK vs K9s is such a dominating hand that it seems counter-intuitive that the presence of AA would all of a sudden put K9s ahead of KK.

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A hand of poker is winner take all. It doesn't matter that KK beats K9 most of the time, because KK also has to beat AA.

Put another way, in AA v KK v K9, KK will be second best hand a ton, but first only rarely. K9 will be the weakest hand the most often out of the three, but is more likely to be first than KK is.
Since best hand is the only one that gets paid, K9 has more equity.

*Excluding splits.