Make sure your file structure is correct. After you enable with JSGME you should not see a new folder with the mod name in the SH4 directory.
My directory structure is:
C:\Steam\steamapps\common\silent hunters wolves of the pacific\MODS\1_TriggerMaru_Overhaul_2-5
with Data and Documentation folders inside.
If you have:
C:\Steam\steamapps\common\silent hunters wolves of the pacific\MODS\1_TriggerMaru_Overhaul_2-5\1_TriggerMaru_Overhaul_2-5
or something similar then JSGME is putting the files in the wrong place when you enable the mod and the game isn't seeing them. If this is the case, just move the folder inside into the mod directory and delete the now empty one. (Some mods are double packed.)
That's the most likely explanation I can think of. The only other thing that comes to mind is that you have to allow the overwrites when you install mods over the top of other mods. Get mods that are compatible with the others you are using and let them overwrite already modified files. You can end up with some pretty tall stacks all working together this way. Some of the SH5 mod lists run into multiple pages.
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