A couple people have had problems running the game in 9x compatibility mode in Win 7. In the topic Inventory graphic placement bug
someone had the same problem under Vista, but they didn't report back if they ever got that resolved.
From Beyond Divinity crash on Windows 7
The inventory glitch is definitely fixed in Windows 7 64-bit by using a compatibility mode of Windows NT Service Pack 5! Yay!
Another person in this topic avoided a crash on startup by renaming the intro video, so the game would skip it. I don't know if that might make a difference trying to get the game going in Win 9x compatibility mode.
Your original saves may not be lost, though they may not be of much use, either. Once items start to show up corrupted they will continue doing so regardless of the system or compatibility mode, so you need to need to either start over or revert to an earlier working save.
Anyway, each save is a separate subfolder in the '..\Beyond Divinity\savegames
Under Vista/7, depending on how the user accounts are set up, if you install the game to the default Program Files path, Windows can create separate savegame folders for each user, and then map that folder to the game's savegame folder (so it will just see the saves for the relevant user).
C:\Users\ %account name% \AppData\Local\VirtualStore\Program Files\Larian Studios\Beyond Divinity\savegames
Changing to a compatibility mode may have altered this behaviour in Windows, so the game started seeing the real savegames folder, rather than the one Windows created under your user folder. You should be able to just move them to the new location with Windows Explorer, if you have any saves that can be salvaged.