When you open MooseEdit, there are 2 paths that must be specified, one to your PlayerProfiles folder (in your My Documents folder), and the other to the game's Data folder (..\SteamApps\common\Divinity - Original Sin\Data). On the right side of the window, near the top, click on the lower folder button and make sure the path is correct.
Have you tried the beta patch on Steam? I don't recall if that caused any problems. The QA version of the game did make changes that cause MooseEdit to crash, so I've changed the 'Game Data Folder' to point to the GOG install of the game. If you have the beta patch and the folder is set correctly, the crash is likely due to the beta.
How does someone acquire the beta patch? Is this an opt-in setting?