I bet if you used a stick, dowel, or some other stiff tool to press on the top round instead of having to use your thumb things would go quite a bit more smoothly Danny. Peeling rounds cleanly off a stripper requires you to have your force as close to the rear of the round as possible. Any force forward of there just torques the base of the round in the stripper clip and causes it to bind.
The added spring and follower of the magazine is certainly not helping either. When the first round goes in, is it contacting the feed lips at all, or is it pretty much free and clear?