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You are running your tests as an output plugin via Sigil and not using the included demo python file right? That demo file is just there for proof of concept and has not been debugged or even tested much on Windows.
I just checked and the epub/zip handed to Bibi does have all of the js code in it. So if you are seeing a problem, that is not the cause.
But again, I can not see any issues at all on my machine with your epub testcase and Bibi (the latest v020).
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