Check your saved game folders and make sure they contain 6 inv.* files. Do items in chests disappear as well? If you start a new game can you pick up a couple things, save, re-load and still have those items? There was a no-CD hack which could cause items to disappear.
Try deleting all of the files in the '..\Divine Divinity\Run\Dynamic' folder.
This folder is used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied from that folder when you save a game. The files will be re-created as required the next time you start Divinity. If there was a corrupt file in that folder, deleting the files should fix the problem.
