You have to choose the two card values you want as your pairs simultaneously. Remember--multiplying the numbers ${13\choose1}{4\choose2}{12\choose1}{4\choose2}{11\choose1}{4\choose1}$ assumes an $order$, i.e. you are counting, say, QQKK2 as different from KKQQ2.
This is why you have to do ${13\choose2}{4\choose2}{4\choose2}{11\choose1}{4\choose1}$. It makes the counting not sensitive to which pair you choose first.