When you turned the run switch "ON", did you then attempt to start the bike? If yes, did the starter turn over and the bike start? The security system just disables the starter and ignition, not the rest of the electrical system. If in your case you can actually start the bike without your one fob nearby, I'd start to wonder if the other fob was hidden on the bike somewhere by the previous owner so he wouldn't have to carry one around with him. There are people who in fact have done that very thing, going back to 2007 when Harley first changed to the proximity system instead of the old fobs with a button. It's not a smart thing to do since it eliminates the security feature completely, at least until the battery in the fob dies.
Jerry