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Im not sure whether it's Windows 10 Anniversary Update bug or a feature or it's a VLC issue/setting but after an anniversary update whenever i select "always on top" option in VLC video settings - windows taskbar would also show up. It seems like a minor issue but the problem is that i usually run VLC player along with some software or a game in a borderless/windowed mode, so now if i run VLC player in "always on top" mode - windows taskbar would overlap the bottom part of a game window. Before the update the taskbar would never show even the player was set to being "always on top".

I know that anniversary update changed taskbar in several ways. Is this how it works now or just some settings got messed up in VLC?

I can confirm that I have the same issue. Before the new Windows Anniversary update, everything was fine.

There is a temporary fix for this - you can press right mouse button on a task bar, select settings and check to hide the taskbar in desktop mode but there's an annoying thin line which remains anyway and it's not very convenient.