Does iTunes jump to the next song if you tap the left or right arrow keys?
Try double checking or changing the fucntion keys, use this as a guide -> Mac OS X: How to change the behavior of function keys
- Choose System Preferences from the Apple menu.
- From the View menu choose Keyboard (or Keyboard & Mouse in Mac OS X v10.5.8 and earlier).
- Click Keyboard, if necessary.
- Enable "Use all F1, F2, etc. keys as standard function keys."
More info about iTunes keyboard shortcuts here -> iTunes 11 for Mac: Keyboard shortcuts
If you haven't made changes in System Preferences > Keyboard, then check iTunes' Help > Keyboard Shortcuts to see methods to do what you used to do with the function keys.
If you haven't made changes in System Preferences > Keyboard, I don't know why they stopped working, but the Help offers reasonable workarounds / substitutions.