Any math wizards out there?

[Erreek]

I was playing with a few friends for low stakes in a home game when a hand was delt that caused some confusion. What happend was the whole cards were delt from one deck, and the flop was delt from another. Now, it was pretty much a family pot to the flop were Player One bet out and got one caller, Player Two. The turn and river went bet and a smooth call. The board was 5d 8d 2d 2s Jd. Player One had Ad 4c for the nut flush. Player Two had Kd Kh for the 2nd nut flush. After the hand, Player Two noticed the flop was delt from the other deck and demanded his money back.

Did dealing from the other deck, although no cards were duplicated, change the odds in any way?