I have a steam version too, and am runnin' TMO too.
When you first install JSGME it will run and set up a folder called MODS right? Make sure you don't install the MODS folder anywhere but here:
C:\Program Files (x86)\Steam\SteamApps\common\silent hunters wolves of the pacific (I am running Vista 64 so your path may not start with x86)
NOTin the data folder.
install the TMO and other mods in the new MODS folder using JSGME.
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