Have you tried running the program as an administrator?
Running as Admin makes no difference.
It also doesn't save any altered keybindings either and all the Save directories on the PC are R and W and none of them are read only.
OK, after a bit more digging around on the PC it turns out to be a Security problem with folder permissions. When you re-install Windows (which most of us have had to do) all the files like Users\*user name*\Documents\My Games\*.* (which is where GOG puts the Save Games) are read only and sometimes your Virus Protection protects this area to prevent ransomware from getting hold of those files and encrypting them. Even changing the permissions from read only just reset as soon as you did anything after resetting them. I set the anti-virus to allow SOMA to write to the location where the save games should be and it's now appears to be working fine.
Hope this will be of some use to someone out there....