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You might consider asking this question in the calibre forum, since you are asking about how calibre works, or in your case doesn't.
I am not a calibre expert at all, but there is an adjustment for line unwrapping which might be set. I also recall reading of a program called briss which is designed to remove margins. I don't know any more than that.
You might also try mobipocket creator to convert your pdf. It will output html which sigil can work with (calibre can too) and which will allow you to see what strange things were done to create the pdf in the first place.
PDF was designed to lay things out on a physical page, which is exactly the opposite of e-readers whose text is designed to flow regardless of changes in text size.
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