I have two problems that are related to third party tools, but which no other program has so I think it's non-standard behavior.
I am using Microsoft TweakUI feature XMouse which automatically gives focus to the window where the mouse is on. Automatic focusing works for WinSCP window, but it also "auto raises" e.g. gets the top window level even if it's under some window. I don't have the "auto raise" option enabled in TweakUI Xmouse.
Before 4.0.6 when I used for example AutoHotkey to minimize the Window it minimized to a small window in the corner of the screen. I understood it should be fixed in 4.0.6, but actually it got worse. Now the window correctly minimizes in the taskbar, but there is no way to get it restored and I have to kill the process.
The tools that I've had this issue with:
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The AutoHotkey script part that minimizes the active window with Win-Z is:
P.S. Thanks for the best SFTP client, keep up the great work! I've been a user since version 3.