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I've had the same issues with BD as you describe... it's touchy, and when importing from apps like Word (even touchier), you often get wonky formatting.
When I create a file (usually in Word), I take care to use standard formatting for the document, text for standard text body, Heading 1 for each title, etc. I also try to make sure Word is handling line breaks and paragraphs the same throughout the document. Often, Word messes these up, though it isn't always obvious, and these messed up formats cause BD formatting to come out wrong. The more effort you put into properly setting up the document before you import it (in whatever original file you're working in), the better your BD file will be.
I've had success both by removing formatting in BD, then highlighting the desired text and clicking the "Title" button to set it... OR, opening the HTML window for a particular section, and manually rewriting the tags (not hard, if you know HTML at all).
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