One additional remark to my comment #55: The pdftopdf filter does the auto-rotation by setting the rotation fields of the pages in the PDF file. This rotation field is ignored by "pdftops -origpagesizes" (as pdftops is called by cups-filters). I have fixed this in Poppler. See bug #72312 and also BZR rev. 7131 in cups-filters upstream.
One additional remark to my comment #55: The pdftopdf filter does the auto-rotation by setting the rotation fields of the pages in the PDF file. This rotation field is ignored by "pdftops -origpagesizes" (as pdftops is called by cups-filters). I have fixed this in Poppler. See bug #72312 and also BZR rev. 7131 in cups-filters upstream.