I dont think the keyboard shortcuts work in mini mode because FrodoPlayer is not in focus, same thing with embedded aps like routis. As for the embeded thing, just click inside of frodo (outside of embeded app) and shortcuts should work again. This is AFAIK by design for the embeded apps, and actually probably better so that way you can use shortcuts for your gps or embeded apps just by clicking in the window.
I believe a way around all of this is if you had an external program that is monitoring your keyboard and pass any shortcuts to a specified application, that way dosent matter what is in focus or not. Im sure there are some apps out that do this, it just hasnt bothered me enough to look for one.