How do you have your movies organized?
Movies --> A, B, C or just all Movies in this one folder? What is the file system Extention? What File permissions do the movies have?
I sometimes have problems reading files when plex is not in the "users" group. It should work without, but I have less problems since that:
usermod -a -G users plex and a service plexmediaserver restart after that.
This!!! My PMS was not detecting any changes in the music or video folders and, therefore, not updating the corresponding libraries. I checked and updated the ACLs but it still didn't worked. I added Plex to the users group and it intermediately worked. Thanks a lot!