Function key defaults are not working

I've ran into an issue where the default function keys no longer work.  The F1 key for instance does not decrease my brightness, nor does F12 increase my volume.  All of the function keys will produce a "thump" sound from the Macbook Air, like I've typed a bad keystroke, or an invalid keystroke for a text field.
What I've done:
1. The "Use all F1, F2, etc. keys as standard function keys" is Unchecked in System Prefs
2. Rebooted, and cold booted many times
3. I've reset PRAM and SMC many times (probably 10 each)
4. I've clean installed OSX Mavericks and the stock install shows the same symptoms.
I'm hesitant to believe this to be a hardware issue because the keys themselves will work if I manually set an action for them (a custom shortcut to open an application for instance).
Has anyone else seen a similar problem or know of any other things I can try?

See if a Safe Mode boot helps.
Startup your Mac in Safe Mode
A Safe Mode boot takes longer than a normal boot so be patient.
Once you are in Safe Mode, click Restart from the Apple () drop down menu then try the keyboard.

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