Make sure you right click the game shortcut, click Properties, click the Compatibility tab, check mark "Run as an administrator" and set the Compatibility to Win 98 / ME.
You are running Vista or Win 7?
Once the inventory is corrupted there is no easy fix that I am aware of. Start a new game, running as an admin and setting the Compatibility mode to Win 98 / Me usually stops the corruption from happening again.
Although murlock never responded concerning the problem, take a look at this similar post and this.
If you reinstall make sure you uninstall the game and delete any directories / files under Program Files\GOG.com\Beyond Divinity. Create a directory outside of Program files, I use a Games directory located on C drive. Turn off UAC prior to installing. Right click the game setup.exe and click "Run as an administrator" on the resulting dialog. On the first dialog of the GOG installer, click the Options button in the lower left corner and direct the install to the Games directory. After installing, right click the game shortcut, click Properties, click the Compatibility tab, set the compatibility mode to Win 98 / ME and checkmark "Run as an administrator".
I would normally suggest backing up your saves first but I don't know of any way to fix the corrupted saves.