Is it a case of the joiners not conducting electricity? Depending on your Atlas track, if it's of the earliest vintage either the rail was too small or the joiners were made out of a springy metal that eventually lost its tension, resulting in drops and unpowered sections. I've heard horror stories about folks having to solder every single joint to get reliable conductivity. Test your rails with an analog meter while the train is running, or press on either side of the joint with your hand to see if the needle moves.
Also, I would just scrape off that black stuff. I had MTH RealTrax for a short while. The blackened center rail inhibited pick-up and the black stuff got all over my loco and passenger car rollers. It's 3-rail track, no apologies needed. The beauty of 3-rail track is that traditionally it IS reliable!
