FIGURED IT OUT!
I know this is an old post but I found a good work around for this. I had an issue where KegaFusion was going fullscreen through Launchbox when I wanted windowed mode. I couldn't change it through Emulator commands, but I set it to windowed mode through the ROM Commands.
1) Edit Game
2) Bottom Tabs select EMULATION
3) Checkbox "Use Custom Command-Line Parameters:"
4) Type -window into box
You would have to do this for each game, but I got the results I wanted and didn't take that long.
Hope this helps!
