There are choices in Acrobat/Reader that affect the scale. Make sure there is no scaling.
This is a known bug in Print Booklet...
It's probably easier to export a normal PDF and print it from Acrobat or Reader (which also has a booklet feature) than to work around it by doing a copy/paste to a new file.
Edit / Preferences / Units & Measurements / Set you ruler units on the units you will always use for editorial design.
This allows you to change you document page sizes without changing the document's unit wich, in my case, was the cause of the multiple page sizes error though I never changed page size. This solution will only will work out for documents created once you set up the ruler's unit or for old documents for wich you never changed the ruler's unit at any point of the design process.
Sintetized: whenever you change your indesign ruler's measurement unit by default defined, you'll find the multiple error page size issue. good luck.