For anyone else having this issue, place the following code in your recipe:
Code:
from calibre.ebooks.BeautifulSoup import BeautifulSoup
for x in ['article', 'aside', 'header', 'footer', 'nav', 'figcaption', 'figure', 'section']:
BeautifulSoup.NESTABLE_BLOCK_TAGS.append(x)
BeautifulSoup.RESET_NESTING_TAGS[x]=None
BeautifulSoup.NESTABLE_TAGS[x]=[]
This will cause the HTML5 tags to be treated like DIVs by the parser (which is what they get replaced with later in the conversion process).