PrimoPDF is a great tool, but for some applications when appending pages from multiple prints it forces rotation of previous pages so that the whole document ends up looking like a pinwheel. This seems to have something to do with the application that generated the page; even appending previously converted PDFs together by printing from Adobe Reader results in the stupid rotation.
I had a solution to this at one time, but didn't document it.
Lacking that information, I now use pdf toolkit to do the appending from a DOS window.
http://www.accesspdf.com/pdftk/