Just found something interesting: I can load without problems my last saved game from .0983. It did use a mod--Heavenfall's--and yes, that's despite "Use Mods" being unchecked, and the required mod files no longer being under C:/My Games/Fallen Enchantress/Mods. However, starting a new game still causes a crash.
There's also a slight, brief stutter to the intro music after "New" is clicked.
Don't know if that will help, but there it is.
EDIT: Just to be clear: .991 crashes to the desktop after clicking "New" from the main screen. Old .0983 saved games will load, and do not crash. And no, I don't play old saved games with newer beta iterations, but I was curious what would happen if you tried them out, given that a new game wouldn't run.