that's a strange one, main issue I've encountered with GBA games was having them refusing to start/display banners, and that was because I was dumb and forgot to install them to both nands so I didn't have a ticket for them
have you patched AGB_FIRM on sys/emu?
afaik the latest rxTools doesn't need AGB_FIRM patched, but I could be wrong
I've been being a noob and floundering at trying to get it compiled all week, hahah. I've resolved to just wait for releases so I don't brick my 3DS. I'm still waiting on the last parts so I can do a hard-mod, anyway