I have a server running samba 3.6.18 and from the windows 7 machine I can see all the files and directories in the share, 2312 files/directories.
But when I install 4.1.6 and view the same share from the windows machine it will only see 1625 files/directories
I can sill access all the files and directories but they are not listed.
I don't know if it's the same issue, but we sometimes encounter the problem that new files in a samba share aren't displayed on windows. Refresh via "F5" doesn't help but if I disconnect the share and reconnect it with the same user as before files are shown. Maybe a caching bug?
Have you tried to repro the issue on latest samba?