The Physics Manager now has a new reset method which will reset the active physics systems. This is called automatically on a State swap (thanks @englercj #1691)

src/physics/Physics.js

@@ -316,6 +316,26 @@ Phaser.Physics.prototype = {
 
     },
 
+    /**
+    * Resets the active physics system. Called automatically on a Phaser.State swap.
+    *
+    * @method Phaser.Physics#reset
+    * @protected
+    */
+    reset: function () {
+
+        if (this.p2)
+        {
+            this.p2.reset();
+        }
+
+        if (this.box2d)
+        {
+            this.box2d.reset();
+        }
+
+    },
+
     /**
     * Destroys all active physics systems. Usually only called on a Game Shutdown, not on a State swap.
     *