Alright seems I resolved this myself.

The problem was that I had a mod that deleted one of the existing default civs (america was deleted specifically by a mod called "Obamanation" with america lead by obama).

My working theory (a complete shot in the dark btw, I don't really know SQL and XML and how they come to make up the game data) is that SQL appends civilizations to a civilization list and the XML-file that deleted america removed it from the middle of the list which messed up the indexes of following civs. It seems to only affect civs added by the SQL-method. I had an outlier SQL-added civ pull through regardless but I would guess it has to do with the mod load order (which you seemingly cannot change yourself?) as in it gets added after the shenanigans caused by "Obamanation" being loaded in.

Hopefully this info is of use to someone else who may seek it.