Their both on NAS drives, but I believe the underlying file systems are ext3.
I can access the one NAS via ssh but the other doesn't have any other access other than web interface.
I've opened the share that's missing the files from another machine and can see all the missing files so it looks like it's just this server mounting it that's stopping me seeing them.
here's my line from fstab that's mounting the share missing files:-
//mss-031cbe/backup /media/backup cifs credentials=/etc/samba/mss-031cbe.smbpasswd,users,uid=root,gid=users,dir_mode=0775,file_mode=0664,noperm,nounix,noserverinfo 0 0
(gotta be honest didn't occur to check from another machine before posting so will be researching google too)