xD yeah... chances are one of the mods hasn't been fully updated yet causing the game to "break".. it could be a simple mod.
I remember when trying to play the European Map in HOtseat, in order to make it more fun I tried to add Orthodoxy and Protestantism (in G&K) to the main game via XML files (not mod files, just the base game files) and it completely messed up the ITR scenario (probably that is the reason they haven't added the two religions into G&K)