Now I know why
I've been using WinSCP under Wine for years too and usually it's fine, but from time to time, it just hangs upon starting WinSCP. Thanks to this wincfg trick, I think I've figured out what is going on when it hangs. I changed the config to use Windows XP mode for the WinSCP that I have (6.3.3) and bingo! it starts and the first thing it says is: New version released, Upgrade/Close/Help. So I guess it was just freezing on user input never arriving, because I never knew it was asking me something.