Okay, that's what threw me for a loop then. I could enable logging disconnect, reconnect, and logging was still on.
What settings is auto-saved? I cannot reproduce that. Please note that logging settings are global, not session-specific.
I think this is new behavior in WinSCP version 4.
When I load the settings from a saved session, change something (to enable logging, say), then connect, the changed settings become part of the saved session. This is not the behavior I would prefer. It becomes impossible to make temporary changes -- like logging -- that aren't intended to be permanent. Can there be an option to revert to the old behavior -- namely that sessions are only saved when you save them?