What could have caused my function keys to stop working?

Most newer microsoft keyboards have a function lock button and by default have the function keys used for multimedia keys. Does your keyboard have such a button? If so, you just need to push the function lock button.

Do they function outside of Windows? Can you cold boot the computer and hit F1, or whichever, key to go into BIOS?

Try booting off a Linux livecd and see if the problem still occurs. If they do, then you know the problem is hardware related.