Probably not doing anything wrong. You may be expecting more of the calibre viewer than it was designed to do. Pretty sure it will have a white background as it's output.
Printing to a pdf output is not the best way to get a professional looking pdf. Mostly handy for quick and dirty photocopy quality stuff. (like a bank statement)
Lot of printing utilities so I am sure you can find one to do what you want if it can be done by just printing to pdf.
Helen
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