As I understand it, the controller regulates the voltage normally, and can charge dual cells if you rewire the charger past the regulator and timing circuit...
(From Quest for Madness)
My standalone charges dual cells fine with only 2 AAs in the charger, and I believe the theory is to charge at about the same voltage as the rating of the batteries, which is why the stock charger is stepped down. The heat, I imagine, is caused by overvolting the batteries. Try charging with just 2 batteries and see if that works...