I can't realy help you for vlc, but I've similar problems with vlc in fullscreen. In my case, the vlc-controlpanel in fullscreen doesn't shown sometimes. It's possible as well, that the problem is connected with my vlc-theme, but I did't test it without theme.
To bypass the problem, I use smplayer and mpv media player. They work for my needs.
Its not really a solution, but in past, I had problems with vlc repeatedly, so I use other players as well.