Hit Ctrl + P to open preferences and click "All" at the bottom to open the Advanced menu.
In the left hand Search panel at the top type: "Always on top" and click "Video" when it appears. In the right hand panel remove the checkmark from "Always on top". Save, exit and restart vlc.
Thanks for your reply but it seems the problem isn't related to On Top option since it was off already,
and it shouldn't even be related to that anyway because it simply doesn't have to be like that at all and other players don't have this problem regardless whether it's On/Off
to be more specific with example, it's like this:
If I put 3 video in playlist and playing game in the same time, everytime VLC load up new video(ex: when first video end and VLC start to playing second one),
VLC get activated "as if I clicked on it" and take control, mess up BOTH video and game play.
This also happens at the repeatation of simgle video.
What really baffles me is that even tho this bug(?) is deadly serious that making VLC virtually un-usable but looks like no one is having problem with this, but only me?
I just don't get it.