IMHO by now posting your
- system HW details,
- sshd_config, ssh_config, and Putty cfg,
- output from running (a separate!) sshd as "sshd <any options> -d -d -d2>&1|tee /tmp/sshd_log" and connecting to it with "ssh <anyoptions> -v -v -v" (try running something like "strace -v /bin/ls <problemdir>"),
- output of a local strace of "ls",
and your firewall script, and maybe some traceroutes between host and client could be helpful...
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