I can't be certain, but I suspect that the mod is not 100% compatible with the fixed maps included with it. I play only random maps from the Faireweather map script, and have had no lockups similar to those described here. My games do often lockup in the late game pre-independence phase, but that's probably because I'm playing on an under-spec laptop with no dedicated video card, and once I have 15 or so large cities and all the attendant units, it just gets too much for my feeble cpu to handle.
My bet is that if you try playing on random maps using the fareweather script, you will have no lockups similar to what you've described.
Cheers, --- Wheldrake