We should be able to export a map that matches the GUI display. If you use scale dependent restrictions on layers you can not rely on this to happen, and have to manually check all output for all feature classes. This was first reported as a bug in 2006, and is still not fixed.
http://support.esri.com/en/bugs/nimbus/TklNMDAyMzU4
"Exports of map elements with scale dependent visibility may differ at higher and lower DPI."
