This seems to be a recent issue, as I'm sure it didn't do this before. Please see this image:
Basically, whenever a progress bar / alert / timeout / any other message comes up, it shows on the wrong screen. If I move WinSCP to another screen, the popup/progress/etc opens up on another screen the next time. Then to my 3rd screen, and it moves to yet another. This seems to be a recent bug (I'm on the latest stable), as it never used to do this.
Is it a bug? Or a new setting that needs to be tweaked to make them open up on the same screen the program is on?
I'm on Win 10 64 BTW