The same thing has happened to me, so I searched up answers on Google, but couldn't find any. In my research, I saw your post but skipped it because it had no answer. Eventually, I got bored with my research and decided to solve my own problem. As I put the batteries in my controller, I saw a spark, and I thought, "They must be burning the little bit of dirt and dust on each other! That's what is making the heat, the burning smell, and the sparks!" So I wrapped one of the batteries in the finger of a rubber glove, since rubber stops electricity, and left the ends open. So the electrical circuit will still flow, but the batteries won't affect one another. After one battery was wrapped in rubber, I put them both in, and there were no sparks, no smells, no heat, and the controller worked like it was supposed to. Although you posted this question awhile ago, I hope that you still may have this problem, see this post, and solve your problem.