Use this solution i've discovered to work for me. But it have still not been confirmed by CDPR that it is a problem on the PC...
I've tried to make them aware of it with no luck!
[Temporary solution]:
1) Find your Wticher 3 game directory and go into \dir\x64 folder
2) Right click on the witcher3.exe file and select properties
3) Go into the compatibility pane and check ON the 'Run this program as an administrator' and hit apply
4) Launch the game and try saving either manually or quick save via F5.
This fix should also save your option changes as it creates the missing folders and files under c:\users\[USERNAME]\The Witcher 3 (remember this might be different on your end due to windows usernames and such)
Also by using the above mentioned fix I don't know if they might at some point conflict with a patch that should solve the issue. But so far updates removes the admin right and you have to remember to apply the above mentioned fix again. Else you might risk losing progress, so do so before starting to play after a patch have come out.
Hope it helps people on the PC with this problem, please post if it worked, so we can get some spotlight on the problem/issue!