The nut between the tank and the bowl should not come in contact with the bowl. If it is touching that could be causing your problem with the rocking tank because it is preventing the tank from contacting the bowl properly. Also, make sure that the are perpendicular to the floor and not off at an angle.
I should also add that the first nut that you put on the bolt should is to be hand tight plus a 1/4 turn. That is in the instructions somewhere if I remember correctly.