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You mean it "saves the cover separately" in the save-to directory.
JS has nothing to do with "adding" a cover to a format.
You posted a question about that in the main forum not long ago, and as I recall the answer was to customize the built-in plug-in responsible for writing out the metadata etc. when saving-to a directory.
JS has nothing whatsoever to do with updating book internals, such as the cover within an EPUB file.
If JS worked for you in your old PC, then it should work identically in your new PC as long as JS has been identically customized. Ergo, it is something else that was not changed in your new PC.
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