But is there any way to get around it? Assigning a different team leader, i suppose, but that's not ideal. Some people don't suffer from it somehow. If i had to guess, i'd say that it has similar origins to how my game settings don't get stored, but i don't know how to fix that either.

Nutaku FKG creates a new dated folder(index_20190227.swf currently) for the settings after every update. I don't think there's anything players can do to keep settings.

The assistant leader is just plain broken. You can see the correct one in the participants list for raid bosses, so it definitely isn't being forgotten.