I had a similar problem when I downloaded an excellent VIIb skin from here, it was packed in the zip for a manual install, not using JSGME, so I had to figure it out, but it's pretty easy actually.
make sure the folder you put in the JSGME "MODS" folder has the correct structure, ie;
SilentHunterIII\MODS\VIIBskin\Data\Textures\TNorma l\tex
with only the last folder <tex> containing files. then disable it in JSGME, and enable it again, then it should be automatically applied in game.
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