Well it's not for the screen per se. There's something about Dualscreens that when loading a rom you have to set the emulator up in one of the options or the game won't play. I can't remember what that is unfortunately, but all I know is that it has nothing to do with the screen ratio. It could be ram or something else, it's been a long time
I'm going to go on a limb and guess that was Save format? I remember PoR not wanting to work unless it was a specific format.
MelonDS doesn't have this issue, once you setup the bios and firmware it's pretty much plug'n'play. I felt I should post it's release simply because No$GBA is fast but inaccurate and Desmume is accurate but slow.