If you want to see how to use JSGME check out this tutorial
http://forums.totalwar.org/vb/showthread.php?p=1009484 and this
http://forums.ubi.com/groupee/forums...3/m/3031058373
Also as Danlisa said make sure that:
1. You have the correct folder structure (see the links I gave you)
2. You're in Port and NOT at sea.
3. You rollback SH3Cmd BEFORE enabling/disabling the mods