I've never had much problem with SmashWords - I do use 'standard formatting' for my books, though, and I think that helps. One should always use H1 styles for their main headers, body styles for their main body text, and so on. If an author follows those kinds of basic starting formats, it works well for all publishers they could want to use.

Lisa Shea, Low Carb and Video Games Editor
Low Carb Forum