As weird as it sounds, I just used TwilightMenu for DS flashcarts. I have the same cart and couldn't figure out how to get in game reset to work with Pokemon games. It works just as well and I don't have any issues when it resets with using the Mystery Gift features.
This tool was a life safer. My Omega Ruby from college refused to boot until I ran the fix like 5 or 6 times. Now I'm back in business. Time to fight the Elite Four.
