Is this possibly something in the headers of the files or other declarations? epub2 vs epub3 is an easy example, but I wouldn't expect that to be it. But, there are other declarations such as namespaces that might. I know I've had some strange behaviour with some wrong declarations (valid elsewhere but not in an epub). I usually expect the calibre conversion to clean them up, but, if they do get through, there might be something wrong.
Another thought is the interface language. I don't know if it should affect the rendering, but, it could be used somewhere to make a choice when language isn't set elsewhere.
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