Media Function Keys Randomly Disabled

Seems like we were able to find the problem through the comments. Chrome sometimes "hijacks" your media buttons for its own functions. A quick google search yielded the following result:

You can set to the keyboard shortcuts to work only when Chrome is in focus:

• Open the Chrome app menu
  • Select Tools > Extensions
  • Click the ‘Keyboard Shortcuts’ link at the bottom of the page
  • Find the Google Play Music section
  • Change any specified media key options from ‘Global’ to ‘In Chrome’
  • Fix Media Key Hijacking in Chrome

Or you can disable/remove the app/extension from Chrome entirely:

• Open the Chrome app menu
• Select Tools > Extensions
• Find ‘Google Play Music’
• Uncheck the ‘Enabled’ box OR click the trash can to remove

Source: OMGChrome