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I have no idea of what is happening - but here is what I would do - have Calibre convert the file to RTF. Then open MS Word and copy the RTF file into Word.
Now you can go to where the text changes side in the file and see if there are any formatting codes which you could fix. In any case, then highlight the whole file and change it to the same size text all the way through, then save the file and feed it back to Calibre and go from there.
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