I have PMS running in the following environment and had the same problem:
Linux CentOS 6.3
HW: Virtual on ESXi
I have the media files stored on a NAS/SMB/NFS server separate from the PMS system. The NAS is OpenFiler and can serve both CIFS/SMB and NFS.
Given that my PMS is UNIX based I opted originally for NFS based mounts from the NAS to the PMS system. After the mounts were setup i could see the filesystems fine on the command line (on the PMS system). I verified that I could Read and Write from the PMS system... all was wonderful with the world.
When I would turn on the ps3 and look for the media, I could see a level of folders but zero files (Video, Audio or Photo).
After fiddling with no success, I set the mounts up to be CIFS / SMB based.... IT WORKED!!!!
I setup an automount for them but any method works fine. Everything looks exactly the same on the command line of the PMS system, but for some reason the files are now visible and playable !!!
If you are using NFS mounts, change them to CIFS / SMB and it's likely to fix the problem....
Hope that helped!