When navigating to a certain directory on the linux side, WinSCP 4.1.5 froze completely, no mouse input accepted. Had to kill it using Windows Task Manager. Upgraded to WinSCP 4.1.6, same problem.
I ssh'd into the linux box, went to that dir, and did a ls -l, didn't see anything strange. Then did a ls -rtlFa (some of those switches not needed I'm sure, just a habit), and then saw a file named '\' (single back-slash) in the directory. After I deleted that file on the linux side, WinSCP now works just fine when it gets to that directory.
Just wanted to let you know. I appreciate this product and the time the developers have put into it.