Check your other thread. You need to apply some config file corrections to SH3 Commander to make GWX 3 work:
http://www.subsim.com/radioroom/showthread.php?t=216166
But this may also happen if you have the Black Sea or Indian Ocean campaign sub-mod enabled last In JSGME. You only need those when you are actually operating there in those regions. It has all the other scripted units in the rest of the world removed to reduce system loading. To transit yourself to the Indian Ocean, you would need to enable the Merged Campaign sub-mod. (There is was no transit route for the Uboats to the Black Sea over water. You just start your carreer there from the beginning.) If you will be operating in the Atlantic or Mediteranean region only then you do not need any GWX campaign sub-mod enabled.