EDIT: Managed to find a YSMenu that does work with my R4i-SDHC and now GBARunner2 is indeed loading GBA roms through Slot-1.
Something strange, why Pokemon Emerald (without any patch or hack) won't run, but it will run Pokemon Fire Red with patches to capture all Pokemon, receiving Mystery Gifts, Evolve Trading Pokemon through Friendship (Gengar, Machamp, Golem, Alakazam, etc.)
Also, Super Mario Advance 4 won't get past GBA PLAYER screen buy SMA 1,2,3 with Color Palette Fix Patches are working.
Metroid Zero won't load, but Fusion will, which is good.
Anyway, thanks for this piece of homebrew. Returning to the DS Scene since leaving it in 2012 feels good!