You have a peculiar place for the MODS folder. Afaik there shouldn't be a JSGME folder in between. The JSGME executable should be in the SH4 base folder, and the MODS folder aswell.
There used to be a version of jsgme that could corrupt your game. But I don't remember which one. But you didn't state your previous version either so this suggestion isn't going anywhere.
I guess the quickest solution is to simply reinstall the game. Little point in salvaging a corrupt install.
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