Quote: "Can my app be compiled to include the media inside the resulting .exe?"
AGK's IDE just cannot do that.
As for the other issue, the file built by the AppGameKit IDE (which is basically a copy of the Windows Player) looks for the 'setup.agc' file to tell it the space available to it. If it does not find it, it defaults to some values in portrait mode (I don't know how it picks them).
So, if you want to use the settings in setup.agc (which probably match what you are using in your SetVirtualResolution command), then you need to copy that file to your desktop as well.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master