Thanks for your report. Though this is definitely not a common problem. So we need more info. Don't you have some desktop extension (or anything else unusual) installed on your Widows that WinSCP might somehow conflict with?

I love WinSCP. But I would love it even more if when I try to transfer a file, the confirmation message did not automatically pop up under everything, making all related windows inaccessible. There's always a question about "Do you want the new file or the old file" and often it is inaccessible. Sometimes I can fix it by moving windows around. But wouldn't it be great if you could just transfer files?