It has happened to me once or twice. The game knows you got a second hit with the optos under the ship. When the first ball is there and locked, it blocks an opto. The second ball is supposed to kick the first ball up and the opto registered the change, signaling the game to release the magnet and give you the third ball. Try it with the glass off and see if it's just a soft hit that failed to move the locked ball up enough. A solid hit has always worked for me, and, yeah, it's a bit of a bummer when you don't get the extra ball 
Marc
Altoona, PA
