Several people have reported problems with the patch not installing. I don't know if anyone has contacted support, yet (at least a couple just downloaded the full install program).
If you don't need another language or a slightly better configuration program, there really isn't very much different in the new release, though. The game dropped support for Win98 (though that shouldn't matter much since the GOG installer requires XP) and no longer lets you right click the menu bar on the bottom of the screen to minimize it to 3 lines (for health mana and stamina), since that cause too many problems with people doing it by accident. There are a couple other minor things I'd have to look up.
The patch checks the registry to get the version number and install path. For this particular error, did you move or rename the folder where Divine Divinity was installed? If you did a system restore or ran an over-aggressive registry cleaner, it may have removed the entries.
There is a registry file in the Larian forum topic
Troubleshooting Tips (& manual install procedure) to add the expected registry entries after a manual install of the disk version. It would be easy enough to get a similar file for the GOG version, if you are familiar with the basics of the registry. GOG support would likely be able to provide something a tad more user friendly, if not an update to the patch.