Welcome aboard!
First make you have JSGME and your mod
installed correctly.
Which mod exactly is giving you trouble? From the sound of it you've probably run into one of those mods that's not JSGME compatible out of the box as it were, but instead has the JSGME mod buried under other folders.
Make sure your mod is installed like this:
Silent Hunter 5\MODS\MyModsName\data\...
And
not like this:
Silent Hunter 5\MODS\MyModsDownloadFileName\MyModsName\data...