Thanks Mitu. I ended up using locate to find any corresponding gamelist.xml for the Naomi folder(s) and wiped them, then I just started from scratch, adding one game at a time and it looks like it finally took the information. I must have missed something in there, but just copy/pasting by hand finally nixed the issue.
It was so weird. Before that it was even naming stuff totally wrong. Like I had MegaMan 3 for NES Playchoice listed in the Naomi folder. And a LOT of the games were being listed as Power Instinct, which is not on the Naomi. No idea why it was generating games that weren't in the folder at all.