If the alignment checks out and the tires are good, and the bike is still pulling to one side, check the front brakes. Jack up both sides and verify that both wheels spin freely with out brake rubbing on a warped rotor.

We had one particularly difficult alignment and no matter what I tried it was still pulling. In the end it was a warped rotor. A slightly warped rotor will usually not cause a pull to one side in a car (unless really bad) but the spyder is a much smaller object to change direction.