I ran into an interesting situation this morning. I am a remote user, and use an SSH tunnel to get to servers inside my company's firewall.
So, to scp I go:
WinSCP -> tunnel on local port -> company ssh server -> target server
This leads to all the "hosts" looking like the same place (localhost).
I've turned off directory caching to get around it, but is there a chance directories could be cached by session configuration or perhaps hostname:port?
Just an idea...I can't complain about your great product...