Some ROM hacks or homebrew applications attempt to swap screens or run "sideways." By booting from the firmware/NAND, melonDS ensures that the register states for the screens are initialized exactly as the hardware dictates. This prevents graphical glitches where a game might load on the wrong screen or appear rotated incorrectly. The "Top" screen setting in the firmware acts as the anchor for the entire visual experience.
: Toggling between Software and OpenGL renderers in the video configuration can sometimes resolve screen-specific display glitches. Quick Setup for DSi Mode To get your NAND running correctly: Howto/FAQ - melonDS nandbin melonds top