The 1.49 patch is the latest version.
Running the game as administrator may let the configuration program delete the file. You can also just manually delete the files in the dynamic folders (but not the folders); '..\Beyond Divinity\Acts\Act1\Dynamic', '..\Beyond Divinity\Acts\Act2\Dynamic', etc. If you still get an error that way (windows can sometimes refuse to delete corrupt files), try rebooting, or boot into safe mode to delete it/them.
The dynamic 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.
Windows Vista (and 7) can move the dynamic folders and the saved game folder to the user directory, and map them to where the game expects them to be (so each user just sees their own saves, if more than one account is set up). I'm not sure if it will do that if you are running the game in Win 9x/ME compatibility mode, though (ie to avoid a potential rare bug under Vista/7 - Inventory graphic placement bug
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