While I can't answer why the CFA, I can partially answer the differences in scores. For the AFT, a HUGE factor is the altitude. For those of us used to sea level, that 1.5 miles feels SO much longer, especially when testing after spending time away from USAFA (summer leave). Also, 1.5>1, seems obvious but for those of us who are not "runners" (ahem, like myself) that extra half mile takes a bit of practice. My 1 mile split is usually pretty good, but then that last half mile slows down if I don't train for the specific 1.5 mile distance. As for the PFT, one huge factor is the pace of the test. You sort of see that with the CFA, but if I remember right, there was a chance to catch your breath between events. The sit-ups to push-ups transition is brutal, as is the push-ups to run transition.
Finally, there is the time to train factor. Fitness is important, but it is easier to let that slide than it is academics. If classes are REALLY tough, and you're close to Academic probabtion, the workout time will probably suffer.