I've learned to ignore the "Vanishing Magnet Broken" message, as it usually figures out that it isn't broken during play.
Also, if you're running the Genie Test, the proper way to do this is to bounce a ball off the front of the Genie to actuate that switch. That initiates the sequence, causing the magnet to grab the ball and vanish, with the ball then actuating the 3rd switch in the subway.