It's quite simple, really...
On the return hills, because the train is so long and the hills are so short, the front of the train crests the hills at a higher speed than the back of the train. So while the airtime on the tallest hills (first and second drops) is better in the back, the return run bunny hills are far better in the front of the train.
The third seat adds to that, because the seat is located directly over the rear wheels of the lead car. This is the pivot point when the car goes over the peak of the hill, which tends to maximize the 'kick' that sends you flying out of the seat in the first place.
Remember, at any given moment, the entire train is moving at the same speed (obviously). The difference is in how fast the train is moving when a particular seat passes a particular point on the track. In Magnum's case, the train is moving fastest when the front car goes over the peaks of the return-run hills. Hence the ejector seat effect. Likewise, when you drop down the first drop, the train is moving much faster when the last car goes over the peak than it was when the first car went over. Hence the better first drop ride in the back of the train.
--Dave Althoff, Jr.