No I don't use any other Mod than these below as far as I know YnEMP don't add any new City States:
- EUI (from the MegaPack)
- Community Balance Patch - CSD Compatibility (v.1)
- Ingame Editor (v.28)
- Yet (not) Another Earth Maps Pack (v.23)
- Community Patch - Civ IV Diplomatic Features Enabler (v.1)
- Civ IV Diplomatic Features - Community Balance Patch Edition (v.10)
- Community Patch - CSD Compatibility Enabler (v.1)
- Community Balance Patch (v.13)
- Community Balance Patch - Civ IV Diplomatic Features Compatibility Files (v.1)
- Community Patch (v.66)
- City-State Diplomacy Mod - Community Balance Patch Edition (v.26)
Don't be irritated by me when I sometimes post additional Mods. I can reproduce the freezes with only those mods above. The problem is the probability. So when you set up YnAEMP and select 22 Civs + 41 City States it will not mean that you will have actually 41 City States in the game. After you started your game YnAEMP's Map-Script will check if there is enough space between the City States (between themself) and if they are not blocked by already existing Civs. So you will end up with up to 25 City States actually.
I don't have any feeling about the reasons or solutions for the freezes. It seems like it is depending on the amount of City States or which Civs are in the game, which will then influence the probability of the occurring freezes. As far as I can see it, it will not make any difference if you select 30 or 41 City States, the probability for a freeze is all the same..
Maybe someone can tell me how much City States can be in a vanilla game (I mean singleplayer only, not via the Mod menu), because there you can select up to 41 City States, too.
The question is why YnAEMP has now a problem with City States, because it is working very nicely without CP etc..