I have this problem as well. There was some discussion over at the JM owner's club thread about this. Bottom line: I have tried new balls, have brand new X,Y nuts, and have adjusted the hand bracket up as high as it will go...nothing seems to help. One of the folks participating in the other thread suggested putting a varistor in the magnet power circuit and try to find the right amount of resistance that solves the 2 ball pick up problem but still allows the magnet to keep functioning correctly. I have not had a chance to play with that yet.
However, I am definitely going to look into nerbflong's suggestion about the whole mechanism sagging over time. That would be a simple fix if it works. Anyway, I hate to say, but I am glad that I am not the only one with this problem-maybe we can stumble on a solution together!