Not sure, but it could be related to Vista data redirection. Certain locations (including Program Files) are now considered more secure than they used to be. To avoid breaking legacy apps, writes to these locations can be silently redirected by the file system driver to another location (I think somewhere under your user folder).
Anyway, make sure you are running JGSME itself elevated. Also, check manually that the files you think are being modified under the SH4 folder are actually modified after installing the mod.
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