There are only 45 × 44 = 1,980 possible ways the turn and river can run out. Order doesn't matter in determining who wins, so for our purposes, it's 990.
I don't know why your simulator ran out over a million hands for this scenario. It's not only unnecessary, but counterproductive, as we can calculate the exact theoretical probabilities rather than simulating to estimate the probability experimentally.
ProPokerTools calculates this one as essentially a coin flip:
Hand | Pot equity | Wins | Ties |
---|
57 | 50.40% | 496 | 6 |
A9 | 49.60% | 488 | 6 |