I've found a slightly updated version of Box2D that ought to be faster and reduce the garbage collection overhead. This should help reduce pauses or stuttering in complex physics-based games. I've done some of my own customisations and the final script after export should come out smaller too.
However since it's modified it might not work exactly the same as it used to. If you could give it a spin and give me any feedback on performance, GC pauses and functionality, that would be great... it worked fine with all the Physics demos I've made, but I don't want to slip a big change like this straight in to a new build in case it breaks lots of games.
Here it is - back up your old runtime.js for the Physics behavior then try pasting this one in: