I'm experiencing some keyboard shortcuts not working in VLC after upgrading to 15.10. The problem persists in 16.04
If I just open VLC with no file loaded, almost all shortcuts involving Ctrl do nothing. Ctrl+O should open the "open file" dialog, but nothing happens. The exception is Ctrl+Q which does work to close VLC.
Oddly, if I open a file then Ctrl–W starts working to close the file, but none of the other Ctrl shortcuts work.
Stranger still, after I've opened a file and then closed it, suddenly all the Ctrl shortcuts start working, but now the menus have changed color and no longer sit within the window title bar.
What could be causing this strange behaviour, and how can I fix it?