OS: Windows 7 (Have observed in WinXP too)
Protocol : SFTP (Thought it might be immaterial here)
Many a times when OS comes back from sleep, the main WinSCP window is unmanagable.
None of the clicks are responsive.
Then I figured out that the password window is lying under the main window and that is causing the issue.
Seems like the focus is on the password window, but it is lying underneath.
I am not good at Visual Programming and don't know what exactly is going one.
If I restore the window using the maximise button then i can see the password window and then I can work with it to cancel or reconnect or stuff like that.
But until I figured this out, it was kinda irritating. I had to kill the program and restart to get the control back.