The only registry entry should be 'HKEY_LOCAL_MACHINE\Software\LarianStudios\BeyondDivinity' and there is no configuration information there, just install path, language and game version.
Did you delete any remaining files (except in the savegame folder) in the Beyond Divinity folder after uninstalling?
This could be a problem with DirectX. Click on Start | Run, type in dxdiag and hit enter, then see if it reports any problems.
