For the longest time (ever since I had set up unRaid) I had an issue with the files saved on the unRaid system showing up as hidden files when viewed in a microsoft windows environment.
Never really liked that. My solution had been to enable viewing of hidden and system files, but it was a workaround. Never really knew why this was happening, until now.
I came across this post on the Unraid Forums. Just need to add a couple of lines to discourage samba to make the files hidden and system files.