I have WinSCP version 3.7.1 on Windows 2000. I will try to describe you some odd behaviour of windows shell (Explorer) when I transfer file on "foreground". If, during the transfer, I double click a file in Windows Explorer, the program bound to the file is not started immediately, several seconds Windows does nothing (the new process is not started, I checked with Program Manager), then the program is launched (with empty document), again several second of wait and after then the file is opened and I can work. This odd behaviour is not present when I transfer on background or no tranfer at all. I am sure that this is caused by WinSCP, it somehow blocks Explorer.
Can you replicate this behaviour?