First, why did you add the [MainWindow] section. That doesn't do anything .
What do you mean by "exit GPS"? I'm not sure how RR works. It sounds like RR is not closing SKINbedder, but it is re-running it everytime you switch to GPS. Is it supposed to exit it? I'm not sure if the problem is that RR is trying to close Sb and it can't, or if RR is not trying to close Sb but still re-running it every time you switch back. If it is the second case, then that is a bug with RR.
CF will run an embedded app the first time you switch to its screen. It will not run it again unless you specifically switch to "full-screen" mode, and click CF's close button on its top border, and then switch to its screen again later. When you do this, CF does properly close Sb.
Sb is designed to be able to run multiple instances so that it can embed multiple different programs in its different instances at the same time (by passing it a command-line parameter specifying the name of the app to embed). I do not want to make it a single instance only app. I would think RR would work with single instance only apps yes/no?
Can you try embedding notepad in RR, typing some text in to it, switching away from notepad, and the switching back to it. If you do that, is your text still there?