I'm guessing here:
Maybe when the spring of a magazine is pressed to its full extent (full mag) then it wants to release that energy more to give it relief and go back to its natural state (empty mag). With a full magazine, that spring is pushing up on the next round with much more force than it would be with 1 less round. Just like how it is easier to load the first rounds into a magazine than it is to load the last couple rounds. When it pushes with more force, it could cause the round to be loaded faster and, possibly, not set completely flat and snug. Then the gun also has that spring pushing the next round up at a high force as well to affect it also.
Honestly, like I said, I'm guessing here but you have got to take all things into consideration. I mean, a 5mph crosswind can cause changes in bullet travel and the force of that spring in a magazine is definitely higher than the force of a crosswind.
Just wait, the guy is going to come back and have some really simple answer and it is going to turn out that I am looking way to in to this because of my engineering background.