I bought the game through my GOG account way back when for Early Access. Now that the full game is released, my wife is playing on her own GOG account. Cloud Saves are working for me and are syncing across multiple devices. But they don't seem to be working for her.

Is this working as intended because she didn't buy the game herself on her own account? Or is there some issue that I haven't figured out. She has her own Larian account and is logged into that when she launches the game.

1st no cloud saves in the Gog system... i assume you mean cross saves

YES patch 1 busted the cross save system

anyone that installed patch 1 yesterday and played / saved files will then get the small hotfix today... your save files are now different and will not sync
i.e, if you other systems now update to patch 1 they will get a different copy of patch 1 [yes the same build number but its different in the files] and your 1st systems save wont sync across