"Always on Top" not working in VLC in Windows 7

It’ll do that sometimes. VLC turns the topmost flag on whenever a video is being played and off when no video is playing, and this toggling on and off sometimes malfunctions.

It is usually fixed by either manually turning it off and then on again, or restarting VLC.

1. Close the VLC player and try running it as an Administrator (on Windows 10, search in Start Menu; right click; then select "Run as administrator")
2. Then make sure "Always on top" in the "View" menu is checked.

This worked for me.