I've struggled with the same essential problem but just found a solution. Check out page 16 of dissertations.umi.com/etd_tutorial_proquest.pdf. It's a manual to help grad students format their PhD dissertations for printing. Worked for me.
I am having the same issue, but the link provided no longer goes to the manual referenced. Does anyone have any other ideas? I've created a landscape document in Illustrator CS4, go to print it as a PDF, and though it would print correctly, when I open the PDF it's tipped over sideways (portrait). What's up with that?