I'm having a similar problem - only after downloading the s patch. However:
When I choose the Play Scenario from the Single Player Menu, it gives three errors saying there was a problem loading worldbuilder file, but still opens the menu. When I select Fall From Heaven II Scenarios it gives me a similar worldbuilder error, but still loads a scenario. When the map is loading (is it supposed to load a map before I chose a scenario?), windows crashes.
I'm using BtS on windows vista. It has a few other problems (although I'm not sure whether they're related to this one); mainly with saving anything. It won't allow me to create save files in the game directory (I save them in another), it won't save any after-game data (hall of fame, etc) and it didn't create any shortcuts when installing.