Ok, I've been searching for more than a couple hours and changing settings but nothing changes.

FreeNAS 9.3 joined to a Active Directory. Group\Admin owns all files/folders in the share 2 Shares, 1st share is readonly for day to day use with user (not admin) on my Windows PC so I can play my files (music/movies) but no editing so it's safe incase I get a virus/malware. 2nd share for admin that I have to mount manually if i need to add/change/delete files.

Today I started investigating because I thought I had a problem with Windows Explorer not showing all folders in the share. Original Post here

After some investigating this is what I found, I'm missing 124 folders. Somehow out of 4752 folders, 124 folders are showing as hidden attribute but only in the readonly share. If I look at them in the admin share nothing is showing hidden attribute. Looking at them from shell on FreeNAS both a hidden and not-hidden folder have same properties. drwxrwxr-x

What am I missing? How can I remove the 'hidden' attribute from the readonly share if I can't find it?