No, the filesystem type of the shared directories don't have anything to do with it... The reads / writes are handled by the host computer.
Can you see anything from a terminal command? Try smbclient -L //server_name . Replace the server_name, of course, or use an IP if you don't have the hosts file set-up.
That command should list any shares on the server_name computer that you can access. If you can see any, then there most be something not correctly configured in Nautilus. I don't use it, so I can't help much there.