The C rand() doesn't warrant same results if run on different machines, even with the same seed.
Problems like this caused lots of problems in Civ IV when trying to run MP games on different OSes (usually Vista and XP).
Regarding custom map scripts, consider Civ IV again. Some players designed new map scripts, for instance PerfectWorld. This map script was totally different from the in-game scripts, and redefined random because the game's default random isn't random enough for its purposes. You'd have to know which script was used to generate the map, be sure the computer where you load the game has the same version of the script as the one which was used to generate the map on first time, which means if you want to write a map script you must version it like hell. Of course, custom map scripts may not be in the game, but it would be great if they were.
The hangup isn't systematic, although I systematically crash on first End turn after loading a game.