I recently spent hours banging my head against a wall trying to figure out why my Plex server couldn't find some new media that I put on its volume in my QNAP.
tl;dr QNAP "Advanced Folder Permissions" turn on file access control lists (you'll need the "getfacl" and "setfacl" tools installed on Linux to mess with them). For more information, see this guide from QNAP.
I must have turned this setting on when I rebuilt my NAS a while back, and it never mattered until I did some file operations with the File Manager or maybe just straight "cp"; I forget which (or both). Plex refused to see the new file, and I tried debugging the indexer and all that other Plex stuff before realizing that while it could list the file, it couldn't open the file, even though its normal "ls -l" permissions looked fine.
Apparently the file access control list denied it, but I didn't even have "getfacl" or "setfacl" installed on my machine (and I had never even heard of this before), so I had no idea what was going on. I eventually installed those tools and verified that while the standard Linux permission looked fine, the ACL permissions did not.
"sudo chmod -R +r /path/to/folder" didn't solve my problem, but tearing out the ACL did: "sudo setfacl -b -R /path/to/folder"
Later, I eventually figured out that it was QNAP's "Advanced Folder Permissions" and just disabled that so it wouldn't bother me again.