I mistakenly tried to select 
"Never see this message again" option and now I can't log into my companies server.
I tried deleting and editing the info in:
    [HKEY_CURRENT_USER\SOFTWARE\Martin Prikryl\WinSCP 2\Configuration\Banners]
 
But if I view the logs, the system still says:
    --- Skipping host startup message (if any).
 
Then the connection times-out and I get this in the log:
    --- Error skipping startup message. Your shell is probably incompatible with the application (BASH is recommended).
 
I think our system is setup to somehow enforce the startup message/banner (they are Gov't system) and skipping it just isn't a wise thing to do. I've completely uninstalled and reinstalled the latest version but it somehow remembers that I want to "skip" the banner. I'm not sure what it does to try and skip the banner, but it's not working.