First off, don't use framesets and frames. Use iframes--frames are deprecated.
Secondly, provide an id for the iframe (or frame, if you must) in order to direct the function call correctly. (You've already pretty much done this, but I'm being methodical.) I wouldn't name it 'top' because 'top' already has a meaning in terms of windows and frames.
From inside the nav frame, parent.insertYourFrameIdHere.fAlert() should work correctly. This assumes two things: 1) The page and the frame contents come from the same domain, and 2) header.html loaded correctly and there were no script errors in it. Script errors or other issues could keep the function from ever being created.