One of Acrobat's (and Reader's) little gotchas is scaling. By default, the Scaling field in Reader is set to "Fit to Printer" and in Acrobat X, which calls this "Size Options," it's "Fit". This reduces (or increases) the size of the document to the "right size for the paper and printer." What Acrobat considers to be the right size is, frankly, anyone's guess. The Acrobat team build their product primarily for document distribution and automation, not so much for the design community. Suffice that for most any design task, the default output size will be wrong.
In the case where Acrobat isn't giving you a choice, booklet printing, you have a couple of different things you can try, having made sure that "Actual Size" or "None" is selected in the regular scaling section:
One is "Print as Image," which you'll find, bizarrely enough, in the "Marks and Bleeds" section of the "Advanced" printing dialog. Use the maximum dpi available. This is most often used to work around problems with Postscript interpretation and transparency, but it can work to avert unwanted scaling also.
Another is "Print to File," located right beside "Print as Image." (You have to wonder about these UI decisions.)
A third is simply to select "Adobe PDF" as the printer.
In the latter two cases you would use that file to actually print the document. This isn't as oddball as it sounds; when working with high-end laser printers using Fiery controllers, it is common to run the document through the Fiery RIP and save the resulting output file in the printer so it can be reprinted on demand without having to open the original file. In that case, though, booklet printing is built into the controller.