Flush Draw Question

[EasilyFound]

This is counter intuitive to me, so I ask. I'm using pokerstove to calculate the winning % of a flush draw/2 overcards to a pocket pair. The winning % when I hold two cards of the same suit is 54%, but the winning % when I have one card of the same suit and the flop is three of that suit is 52%. I would have thought that it would be the same. Why not?

Here is the cards I was using for both examples.

#1. A [img]/images/graemlins/diamond.gif[/img] K [img]/images/graemlins/diamond.gif[/img] vs. Q [img]/images/graemlins/heart.gif[/img] Q [img]/images/graemlins/spade.gif[/img] and flop of 2 [img]/images/graemlins/diamond.gif[/img] 7 [img]/images/graemlins/diamond.gif[/img] 9 [img]/images/graemlins/spade.gif[/img] = A [img]/images/graemlins/diamond.gif[/img] K [img]/images/graemlins/diamond.gif[/img]d being 54% favorite

#2. A [img]/images/graemlins/diamond.gif[/img] K [img]/images/graemlins/club.gif[/img] vs. Q [img]/images/graemlins/heart.gif[/img] Q [img]/images/graemlins/spade.gif[/img] and a board of 2 [img]/images/graemlins/diamond.gif[/img] 7 [img]/images/graemlins/diamond.gif[/img] 9 [img]/images/graemlins/diamond.gif[/img] = A [img]/images/graemlins/diamond.gif[/img] K [img]/images/graemlins/club.gif[/img] being a 52% favorite.

(Numbers round up or down where appropriate)