I had a similar problem and the issue was that Gnome would capture the media keys before they reached VLC, to fix this you can go to "System->Preferences->Keyboard Shortcuts"

There you will see a header called sound (Expand it if needed), and remove the key combinations you want in VLC from there (You can disable them by clicking on the item and then pressing backspace).

Only problem with this is that any other applications that do use Gnome's built-in handling won't work anymore with the media keys, unless you add them again (Which in turn breaks VLC again)