I discovered today that DraStic, the Nintendo DS emulator – also supports creating shortcuts for games; and somehow they’ve managed to overcome the problem – whether the emulator is in the main menu, or within an existing game – whenever you click a shortcut the respective game always loads.
What about if the shortcut first kills the activity, or the entire task – and then launches it from the beggining? Is that possible? It would be a way around the problem.
Failing that, you could get in contact with the DraStic dev and ask him how he did it. I would do it myself, but I have very little experience with the Android OS and davlik and I fear that many important details might go over my head.