I moved my taskbar to the top of my desktop. A bit mac like :P
If I close WinSCP maximized and restart it, the window opens with top = 0px.
But it's height is desktop height - taskbar height. So at the bottom I can see as much desktop as my taskbar is height. If the taskbar is at the bottom there is no problem.
WinSCP version: 4.1.0 Beta
Windows XP Home SP2