I just installed the GOG version, rebooted (don't recall the installer asking...) and installed the 2.2.0.4 patch (game version 1.0.51). The patch seemed to stall a quarter of the way through (maybe just a large file), but finished ok.
Someone in the GOG Divinity forum mentioned getting an error until they re-installed the game and rebooted before installing the patch (and said the main install package has been updated, as well, so if that doesn't help, a full re-download should).
Did you ever install the 1.0.47 patch? If not, this might explain why it worked for you.
