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You've created an 'image + hidden text' PDF file. So in a single page you have the image graphic on the top with the roughly placed OCR'd text behind the graphic. I agree that for OCR'd content this is a convenient format, however for reading on an RMSDK reader this will cause exactly the problems you described, since when going into 'reflow' mode (which is what increasing the font size on a Sony Reader will do), the layout in the PDF file is ignored and the text from the file along with any graphics will be rendered - giving you your double.
The only obvious work around is to strip the graphics from your PDF file (assuming you want to do a reflow - because you are changing the font size).
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