Omni,
Even on massive maps, the Civs will move, settle, etc.
You have the 'Ghost Civ' problem. Stems from the scenario getting messed up internally while it was being created. Generally, although not always, this comes from not deleting the original settlers before playing with the 'Set Start Loc' options.
POSSIBLY, if you go back in and delete all the settlers, then set the Start Locs again, it might fix it. Although, quite often, once the scenario gets messed up, it is toast and no longer usable.
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