Yeah a lot of people have this minimum spec problem with civ as a whole (I do) Have you tried turning off the "Show minimum spec warning" in the .ini file? I think if you turn that off it solves the problem I think it is something to do with newer operating system and civ and new hardware etc. the game things it is not up to spec, so warns and drops everything, I think if you turn that off it stops 'helping you' and just gets on with the game at whatever specs you set because obviously your computer can handle it. I don't know for definate that it solves problems between mods, but it definately solves the message pop up. It is quite a common issue people have I think. Also I haven't tried custom games, so it might be something in there that causes clashes issues, but again I don't know why!? I always go 'Play Now'.