Douglas,
This is how the eclipse export project export works – it’s an exact copy of the project as it exists in your workspace into a zip file or another location. This is something provided by base Eclipse, not MyEclipse. The JAX-WS libraries are referenced and not copied into your project which is why the same references exist in your export.
If you want everything to be exported, you can try the WAR export, but that is more suited towards deployment and not re-use in another workspace.
The only suggestion I have is for you to perhaps create a user library with the same JAR files in it and stop using the ME libraries – remove them from your build path. Note that here too you will need to redefine your user libraries in your home environment, Eclipse will not export the contents of these.
Hope this helps.