Some applications like to reset their own position occasionally, or don't take kindly to being resized from an outside process. WinSCP is an example where workspacer tries to resize/position the window, and WinSCP itself listens for the move event, and moves itself. workspacer gets that second move event, and cycles back and forth forever.
For the few cases where it doesn't work right now, I have ignore routes setup in my config file (so workspacer will just ignore any matching window). I should probably make a list of the few common apps that are weird.
Martin Prikryl (the WinSCP main developer) is quite active on their forums and on StackOverflow questions about WinSCP; might be worth asking why or if it could be turned off;
