GOG probably doesn't have the patch up yet. Usually takes them a day or two.
My suggestion would be, once the versions are lined up set your steam version to only patch when you launch.
Then in the future launch the game directly from the EXE in the STEAMAPPS/Common/Divinity EE/Shipping folder. Should be called EoCApp.exe. That will prevent the steam version from auto patching and getting ahead of the GOG version.
This of course will only help if you are playing with someone you know.
Also achievements and stuff won't work.
