You have a lot of files with strange encoded names like:
Your filesystem, transfered from older samba servers, contains files with windows-1252 encoded characters ibn their names, who won’t be displayed by samba.
Use the magic convmv tool:
# convmv --notest -r -f windows-1252 -t utf-8 /path/to/your/data
Thank you, Bjoern JACKE!