Not sure if you're still following this thread, but another major factor is that only a very small percentage of hands actually have much monetary significance. At a full table in limit Hold 'Em, a strong player will fold ~80-85% of his hands preflop, and of those that go to the flop, only ~40% of those go to a showdown, and only a fairly small percentage of those are medium to large pots.

Luck on these bigger pots has a huge impact on overall win rate, but in a set of 100,000 hands, you may only be involved in 2-3000 of them, and you may only expect to win something like 400 or 500 (very rough estimates). Maybe that helps explain why there's more variance than you might expect in a seemingly large sample.