Naw, the issue I had was not having
enough flags. I think the game has a hardcoded minimum number of flags that it uses. So I think it was pulling up flag0300. jpg or something, except it of course didn't exist. I've (hopefully) temporarily circumvented this by copying flags I already had and adding them to numerical format. That seems to have done the trick, as the 20 empires I SM'd all had proper flags
I don't plan on playing with more than one or two NPRs per game, so having copycat empires won't be a huge problem. Eventually I'll have to replace them with proper flags
Thanks for all your guys help!