Updating from 2015.12-1 to 2015.12-3 and I got the Samba message as well. Used the SSH and command line upgrade to workaround with no issues.
My concern is that I support several others running OSMC (with the Samba server installed) who won’t have the skills or knowledge to do any kind of SSH workaround and don’t have USB keyboards.
If one has installed the Samba server package, is some form of workaround going to be mandatory when upgrading? I realise that the latest update will prevent the problem in the future, my concern is preventing (if possible) it happening now, for this specific Samba case.