Depending on the length of your femur vs. your tibia, you might not fit the "typical" WSD set up. (which tends to be designed for a women's proportionally long femur vs a man's proportionally shorter femur)
Leg length (femur + tibia) isn't the only factor for bike fit, though it seems to be the one the shops look at first. The ratio of the two bones (femur vs. tibia) determines where your knee is relative to the crank and what muscles your body has to fire to get power during different phases of the pedal stroke.
If it feels wrong, your body will probably try to move your butt/hips to adjust the knee flexion, since it can't move your feet. (they are stuck with the pedals right where they are)
Perhaps your femurs aren't the extra-long versions, so the seat feels too far back for you because your knees aren't getting to center themselves over the pedal axles at the right times.
I have the opposite problem (looooooong femurs and the seat scootched way far back), so I might just be talking through my hat here.
Head back to the shop and make sure they look at the whole leg and the postion of the knee through the stroke.