I have an FNP-40 and have not had that problem. I deliberately load my magazines to full capacity at the range and when I chamber the first round I top off the first mag to test the guns ability to feed with 14 in the mag. I'm over 1,000 rounds and the gun has fed FMJ and JHP without a problem.
Sounds like you have a 9mm if you're removing 2 or 3 and still have 13 or 14 in the mag. Can't comment on that, because I don't have a 9mm, just the .40.
How many times have you FULLY loaded and unloaded the mags (not firing, just by hand)? What kind of failure is happening (will the round not strip from the mag, is the nose of the round diving or climbing)?