I have an old 1400 Winchester (grampa's) that would do the same thing, but my problem was age and wear. The shell stops (on the side of the trigger assembly) had press pins that were worn out and loose, a couple tacks with the wire feeder kept them in place and it now works 100%. What happens (at least to me) was that the stops did not keep the shell far enough in the mag tube to let the lifter drop all the way down and pick it up, thus, one round would fall to the ground, then the lifter would come down and the second (actually third) round would get picked up by the lifter. I essentially had a two shot semi-auto and was not going to live with that! I would start there myself.
These are what the shell stops look like, and you will see how they hold the shell in place with the bent lips on the ends of them near the magazine