I blame your unit designs.
In all seriousness it may be that since you have duplicate unit designs to the ones that are now in the game it is causing an issue. I had worried about that but I changed the internal name of all of them to try to keep that from happening. Hmmm...
Could you try renaming your "My Games\Fallen Enchantress\" directory to "My Games\Fallen Enchantress.old" to see if it fixes it?