That "Marathon" map is really awesome!
Funny thing: I fix those errors simply using the original editor in the CivIII backup folder I did some days ago on my hard disk, before installing some scenarios and mods (Aoi II, CCM, Flintlock). Maybe the Flintlock interferes (?) Anyway, solved
I managed to use CCM3 for that map, and I think it's a superb combination!
I just have a couple of questions, hoping not to bother:
1) Is the 512 cities limit still active in Flitlock-CCM3? Because with 20 civs and a so big map you could easily reach that number. Same for unit_limit, I don't remember if it was unlocked;
2) If the city limit does not exist anymore I think it could happen a problematic spam cities foundation when Settlers start to be simply produced by the city (I remember it happened with a tech in CCM2). Is it possible, with a little personal change, to disable settlers production and mantain the automatic production every 20 turns, without creating errors or crash to the CCM game? (by the way: this mechanich is the bigger gamechanger in CCM, great idea!

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3) Is it possible to disable also the exchange of technology between Civs? That's because if a Civ missed some exchange in the first Era, it remains fatally backward, and Civs that grow on islands, South Africa, America tends to remain very weak (that could be realistic for sure, but personally I would prefer to disable that option if possible)
I'm playing as Japan with an autorule: colonize only islands in the South Asia - Oceania and don't set foot on asiatic dry land till to the late game. Beautiful game
Thank you again