Thanks for sharing this!
Before posting, please read how to report bug or request support effectively.
Bug reports without an attached log file are usually useless.
OK, will consider this.
Did you try to enable keepalives to prevent the disconnects?
Yes, the "Disconnected" error message flashes the taskbar button. But it does that on purpose.
I do not think WinSCP activates a window during reconnect. Or what exactly do you mean by "activate"?