Sounds like you forgot to check the "Include Blank Pages" box in the page setup so ID is ignoring the ones you added and inserting its own.
Thanks so far.
I am unable to find the "include blank pages" unles it is the "print blank printer spreads". I have ticked this box. A workaround I come up with is to put a white box on the blank page. It then looks and prints properly.
I am using 5.5 with mac os 10.6.8
I'm on Windows, so what you see may be a little different. At the bottom of the Print Booklet dialog is a "print settings" button which, when clicked, opens the regualr Print dialog. In the Options section at the bottom of the General pane you should see a checkbox to include blank pages.
Thanks you are spot on and fixed the problem.