Well, I fixed it. It looks like the default emulator was causing a problem. I swapped it to libreto gpsp and it started working. I thought that was the default but I guess not? Either way, it's working now so if anyone else has this issue, this is how I solved it.

Well, apparently I was wrong about the other Harvest Moon game working as well. I just tried it and it is NOT working either. Games that are DEFINITELY working include Grand Theft Auto Advance, F-Zero Maximum Velocity, and Legend of Zelda - A Link to the Past. They were played for at least 10-20 minutes. So I'm really confused as to why Harvest Moon would not work, especially when they work on a RPi2 RetroPie and this is a RPi3 Recalbox (which has been much more stable, BTW).

I am trying to get Harvest Moon More Friends of Mineral Town to work on a new Recalbox build. I am using the exact same ROM from a RetroPie build and it works perfectly on there. But on Recalbox, it freezes within 60 seconds of starting it. Other GBA games work fine, including Harvest Moon Friends of Mineral Town (older version of game, boy character versus the girl character in More Friends). Any suggestions? I have already tried: checking BIOS (yes, it's in there and yes, it matches the checksum) and other ROMs for this game (all of them freeze)