Also try adjusting height and angle of the seat, perhaps raising it a tad.

MIne's a tad low right now (but, alas, fused so I can't get it loose yet... now, if it's stuck, how come it's gotten lower??? Aargh...) and my butt and knees are what talk to me, and it's only a few hairs too low. It's easier to get into a "sitting too low" situation on the more upright bikes.