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Your problem isn't actually within SC2. The checkbox to disable OS keyboard shortcuts has nothing to do with the function keys, its to do with keyboard combinations like Command+M which toggles SC2 in/out of fullscreen mode. You can disable this if you don't want to accidentally trigger one of those commands while playing.
As you have it at the moment, the function keys are performing their functions and not registering as f(number) keys, you can temporarily switch them to f(number) keys by holding down "fn". To invert this setting, and have them default to f(number) and use the "fn" key to access mute, volume change etc. go into System Preferences -> Keyboard and check the box that says "Use all F1. F2, etc. keys as standard function keys."
Sorry, but this is wrong. It has everything to do with function keys—if you have F10 set to toggle Mission Control or Dashboard or something. But he's right about the rest: you're not using your F10 as F10, but as the little icon on the same key.
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