Have a link the sites causing the issue? They may have setup a printer friendly stylesheet, where there is no colors are specified. Even and option like "printing to" PDF (Quartz or Acrobat) is going to utilize the print stylesheet, as you're still printing the page (at least according to the browser).
You could try enabling "background" printing if you're talking about block of colors missing. File>Print then select Safari (from the dropdown that defaults to Copies & Pages) and make sure the Print background box is checked.