I ran into something like this. It looked fine in Word as an rtf and (saved as a filtered html) it looked fine in Firefox but on the reader it seemed as if it was only using the center 50% of the screen. It seemed like left and right margins were set to 25%. Upon examining the source html I found some sort of html code labeled ??block?? and it was set to 50%. I eliminated all of them, and most of the rest of the junk that Word had inserted into the html. After that it looked fine.
Sorry I couldn't be more specific. I went crazy and eliminated most all of the Word stuff then dragged the html to Calibre and it finally converted fine.
Good Luck!
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