How is it that you're telling that it's only hitting the edges? Do you just see the metal streaks on the edges? If so, it's very possible that (having just gotten it) that you're holding the knife at a slight angle to the stones (i.e. not at a perfect right angle), which would cause it to hit the edges rather than the flats.
I think the important bit about the flats is that if you're doing it right, you're putting less pressure per unit area on the edge, therefore making for a smoother cut. I wouldn't worry too much about this unless the stones are actually malformed. Take the two stones out of the base and put them together flat-to-flat.... they should fit together smoothly. If they do, then it's your technique.