Sounds like you had the default civ count dll originally, and then when you reinstalled you choose the 43 major civs one.
Reasoning: You can only have 63 civs in a game max. This includes barbarians, city states, and major civs. Aka if you choose the 43 major civs you can only have 20 or so for the city states. If you use the default dll you get 40 or so city states. You cannot have both. In fact I am thinking about making a version of the dll with only like 30 civs, because i like having alot of civs but I want more then 20 city states so.
Hope this helps,
Bob