Have you tried to find out, if the problem only occurs when working from your current user account? Tr yto export jpegs - original size, while logged in from a different user accouns, for example the guest account. Does that work?
If yes, then it might help to remove the user preferences and, if necessary, the presets as described in the Aperture 3: Troubleshooting Basics, see the paragraphs: "Delete the user preferences" and "Move the user created presets, keyword lists, and so on..."
In the Info panel, what is the value for each of the fields "Pixel Size" and "Original Pixel Size"? And what field are you getting the value 16MB from? And what do you mean by "If I use the TIFF setting it performs as it should"?