When you use JGSME to enable a mod, it basically works like this: the program lists the folders inside the MODS directory. You choose which ones you want to enable. As you enable each one, it takes the files and folders inside each mod folder and copies them to the identical place within the main folder after making a backup of each file that's replaced. Disabling a mod simply replaces the files with the backup copy.
The result is that you must have the identical file structure within the mod folder as within the main game. The vast majority of the files are within the "data" folder, so you should have a "data" folder within the mod folder, with all appropriate subfolders under that. I have a habit of extracting the mod files into a folder already named after the mod, and most of these automatically create a folder named after the mod on extraction, which screws up the JGSME installation. Check and make sure you haven't done something like I did. 
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We, the unwilling, led by the unknowing, are doing the impossible for the ungrateful. We have done so much, for so long, with so little, that we are now qualified to do anything with nothing.
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