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I always convert docx to epub2 first, then to whatever else. Never had a problem, not even with ToC, unless the docx was broken.
Heuristics is extra stuff to try and convert broken source. Better turned off and fix source. Kovid has a few times told people to turn it off.
I don't know what flatten epub does, but as all conversions of unbroken html, txt, docx, mobi,epubx and azw3 work without it for me, I suggested turning it off.
Similarly unless you have crazy images, "tablet" profile is best even for 4.3″ screen epub or 6″ ancient mobi Kindles (167dpi?).
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