I think I'm seeing what might be going wrong. I just made another PBEM for this, using the Cnsrv mod with straight r9445, and the default UserSettings folder (IE, empty but the one folder). Altered the BUG settings during the 1st turn of the PBEM game. Game saved as it does when turn ends, and closed Civ4. Checked UserSettings folder and it was still completely empty, except for that default folder.
Launched using the created save game file (see below). Game loads fine. Check the BUG options in-game, and they are almost entirely wrong, but greyed out. Close the game without saving. Check UserSettings folder and it has lots of files in it.
Thus what seems to be happening is that, like I just did not do, JosEPh did not set the BUG options in a single player game prior to making the PBEM game, and the BUG settings did not save properly in game. Then, when the next player goes to load the game, their computer creates what it considers default BUG settings, which means that the files in the mod folder are now different, and thus the mod does not load. Except that it loaded for me. Save attached if anyone wants to see if it will load, and if it does, check to see if the BUG settings are correct for what this game is supposed to be. Specifically, No Storms and Multiple Religion spread should be on, and Sea Tunnels should be off. There are lots more, but those I recall offhand.
Thunderbrd, did you set the BUG options in-game for the 1st turn of the Prgsv MP, or did you do a SP first? If the former, they are probably wrong for subsequent players.