I think the problem here is a lack of focus. "Focus" is the term us computer geeks use to describe which control, window, or other peice of UI the user is actively interacting with. When you're on the map, the map has focus, and when you mouse over a synth the focus remains with the map. It's not just the ~ key that wont work with the synth - all the shortcuts wont work (arrow keys, spacebar, +, -, etc). To get the behavior you are expecting you first need to give the synth viewer focus. This is pretty simple - just click on it. Make sense?