My bad, I meant V42, of course. I don't think v41 is even downloadable from the main c2c dl page.
How did you merge it?
Here's the file that I keep overwriting the current mod update each time with.
Just unpack it and overwrite if prompted.
It only changes the Custom Civs roster, which is the thing you need in the first place.
The original file has some additional stuff, which now is outdated and probably wasn't even needed to begin with.
I mean, these are just Custom Civs, so why was there a file for buildings included to begin with?
Use THIS one, and it definitely shouldn't glitch whatsoever.
Use it on a CLEAN install, or after VERIFYING the other "mods" to be working.