The addition of the extra css isn't causing the problem. It might cause other problems, but, they will be when the book is rendered on the device.
What it looks like is that the parsing of the text has changed. Somewhere there is something that is seeing the "<br/>" and deciding a "</p>" is needed after it. The extra "<p>" is added later, probably as part of a beautify function, to fix the error cause by having unbalanced tags.
I can see the changes in the plugin to get the code out of the books and parsing it. I haven't dug down to see exactly what else is going.
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