Are you adding these as epub or kepub? If the latter, how are you doing it. If you manage to get the books on the device as kepubs but do not get the spans that Kobo requires added, you would get the behaviour you are describing.
Looking at the code, I don't see anything obvious that would cause problems. The self-closing span is not something I can think of having seen, so I'm not sure how it would affect things. I don't think any of the CSS will affect it.
Are the books anywhere we can look at them? If they are legally downloadable somewhere, I can have a look. Or you can use the ScambleBook plugin to produce a version you can safely upload here for others to test with.
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