For some reason the devs responsible for the latest OSX update have decided that the media buttons should control whatever media player last had focus. This means that they now seem to have a mind of their own and do not solely control iTunes, which is a great big PITA if you ask me. It's evidently not a bug, but a feature - lol
Fortunately Milan Toth has written an app that reverses this annoying 'improvement', which you can download from the link below.
If, like me this 'improvement' has stuffed up your work-flow, please feel free to do as I did and let Apple know using their feedback form ;)