You know, I was thinking, and maybe the arm swing is what breaks my two-footed jumps - if you happen to lower the arms at the same time as the legs are amortizating the plant, then the force generated by the amortization of the bodyweight + the additional pressure created by the arms "pushing you" into the ground could possibly overload the quads and mess up the jump.
Also, if the arms and upperbody aren't moving more vertically and if the timing is bad, the upperbody will go forward and you will jump forward (will not be able to convert from horizontal movement to vertical movement).
I should film my two-footed jumps from the side and compare them to someone else at the same moment in time and see what I find out.