Menu bar for many programs such as VLC have moved to my panel.
What is causing that?
That must be 'global menu', it is part of the Cupertino layout in mate-tweak.
It uses appmenu-gtk2-module and appmenu-gtk3-module but I don't have the slightest clue how to disable that, other than change the layout in mate-tweak . I've never used it.
Right-click the menu bar in the panel and click Remove from Panel. That should solve the issue right there.
Doh...is it that simple ? 
that does not work.
I solved the problem by using Mate Tweak and changing the panel layout.
I did lost most of my icons which I have recreated.