Are you running the game as administrator? In the compatibility options you could also try disabling desktop composition.
Did you try reinstalling the game somewhere outside the Program Files folder? (c:\games\Beyond Divinity or something)
Try disabling Aero. Maybe that could help when switching away from the game and back.
The version number doesn't get updated when applying the 1.49 patch to v1.47 of the game, presumably since there were no changes to the game itself, just the removal of the copy protection. If you can start the game without the CD/DVD in an optical drive, then the patch was installed properly. The version number does get updated 10 1.49 when installing the patch over an earlier release of the game.
