I mentioned deleting the files in the dynamic folders in the other topic on this problem.
'..\Beyond Divinity\Acts\Act1\Dynamic', '..\Beyond Divinity\Acts\Act2\Dynamic', etc.
These folders are used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied to those folders when you save a game. The files will be re-created as required the next time you start Beyond Divinity. If there was a corrupt file in those folders, deleting the files should fix the problem.
In the other save I looked at where a crystal was not dropped, it was not due to a corrupt file, but it couldn't hurt to empty the dynamics folders.