First step, double check that you didn't get a doubled folder in your mods folder.
This is what you want:
Code:
SH4 THIS IS THE CORRECT WAY
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->MODS
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-><mod to install>
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->Data
Depending on how the mod was zipped and unzipped, you may find that inside the "<mod to install>" folder, you have another folder called "<mod to install>". Inside this folder you should find the "Data" folder.
Like so:
Code:
SH4 THIS IS THE WRONG WAY
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->MODS
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-><mod to install>
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-><mod to install>
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->Data
In this case, run JSGME and disable <mod to install>. Rename the outer "<mod to install>" folder to "<something>". Drag the inner "<mod to install>" to the "MODS" folder, delete the "<something>" folder. Run JSGME and enable <mod to install>.