What happens currently is that when you switch layer, all 3D View windows switch to that layer.
This is sometimes annoying when you edit an object in a layer and have to switch back to the game
to press P and test the changes. Then go back to the object, then back to the game, etc.
Could it be that one window shows a layer and the other window shows another layer ?
OMG! I have been using blender since 2.27 and I never ever knew that…you just saved me about a month of work. I am constantly switching between layers(and scenes…no way around that one though)…