I use a ssh proxy tunnel for my networking (read: cheap VPN) and recently Cyberduck has been responding with an error: IO Error: Malformed reply from SOCKS server.
I also noticed that the ssh proxy connection posts a message saying channel x: connection failed: Connection Refused.
Now Cyberduck seems to be using the system-wide SOCKS proxy settings but before didn't seem to mind when I had the service set up, but now refuses to connect until I disable the system-wide proxy settings.
I don't know if it works fine for a regular SOCKS server (SOCKS4/5?) but with the dynamic proxy mode of SSH included with Tiger (10.4.5) does seem to fail it.
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I am also seeing this in the very latest version of Cyberduck (2.8.4) and OS X (10.5.2). I have a SOCKS5 proxy set up locally via "ssh -D some.computer.I.control" and I have my OS X network proxy settings pointing to it. Same exact error- "Malformed reply from SOCKS server." Please fix!