BiggieShady: The GOG client app on a GFN virtual machine says the 4.0 update is installed, however the game files are obviously not updated since it runs v1.32
It was updated soon after release for the steam version. One thing that people may have missed is with the updated version they merged the game for the three store fronts. It said in the update notes for the games that you would need to delete the Game of the year edition if you were using it with GoG or Epic and readd the unified version to your game library. Once you do this, you should get the updated version.
Extra extra note:
Today in GFN there two Witcher 3 entries in GFN. One is Steam only, and the other is Epic/GOG.com. NVIDIA will be combining these into a single entry in GFN for when The Witcher 3: Wild Hunt — Complete Edition launches. There should be no impact to user saves, country availability, etc. The only change that Epic/GOG.com users will see is that the game will be removed from their GFN library. This doesn’t change their ownership on the other stores, users will just need to add it back to their library or play it again.
If it didn't do the deleting and have you readd the game, maybe this is the issue?
Edit:
Looks like gforcenow is aware of the issue, found this on their site:
The Witcher 3: Wild Hunt GOG.com version is not updated yet to the Complete Edition. We are working to update it as soon as possible.
So, hopefully soon.