I seem to recall Martin Brundle talking about this recently in that the packaging for KERS is extremely tight, fitting it within the body of the car and allowing for room with the driver. He was speculating that one possible reason why Mark Webber seems to have had many more KERS issues than Vettel overall is that he is one of the tallest drivers and literally to allow room for him in his survival cell means that things are just a little tighter in packaging around the cockpit area meaning there is less room to adequately cool the KERS batteries and they often overheat.
Supporting this idea somewhat is that Adrian Newey was not a fan of KERS when it came into the sport and pretty much said, "well if we have to use it, we will have to make it fit within my design, I am not going to compromise the aerodynamics by changing the bodywork to accommodate it."
It was funny actually looking at the podium on Sunday, Marks' head was almost level with Sebastian's even though he was a step down. Martin Brundle was also talking about that they should do more in the regulations to stop tall drivers being disadvantaged versus the smaller ones on these issues by making minimum cockpit sizes and vehicle weights such that it makes no difference whether you are tall or short. Obviously it should be about driver talent, not whether you are really small..
I know that Kubica, Hulkenberg & Button have all had issues in the past due to their height.