My Mac media keys are completely disabled. I originally disabled them far too long ago to remember how exactly I did it but I remember it was via the terminal that toggled a switch not available anywhere else.
To be more specific all of my function keys function properly without use of the fn keys and the media keys do nothing even with the fn keys.
Best Answer
to re-enable media keys you can use:
launchctl load -w /System/Library/LaunchAgents/com.apple.rcd.plist
explained in this article