I've also found this to be an issue with a mix of letter and 11x17 on Windows 7 & XP.
The problem occurs under the combination of Choose paper source by PDF page size and Orientation - Auto portrait/landscape. To correct this problem, set the Orientation radio button to Portrait or Landscape instead of Auto. This will cause 11x17 pages to print upside down, so we would need to rotate them 180 either in the document or in the print driver. Also note that any landscape letter pages will print upside down as well. Hope this helps.