Why are you using this workflow? There are usually better ways to create booklets.
How many pages in your file?
What better ways?
As I said, I have a 60-page book. The same problem occurred with a four-page test file, and both before and after updating InDesign to the current version.
In previous years, I could do it directly from InDesign or even PageMaker, but I haven't found a successful way to do it with the newer software. If need be, I'll manually move all 60 pages around, but I had hoped not to have to do that.
Easiest way is to export a PDF normally, then use Acrobat to print the booklet, but there are scripts for InDesign for simple impositions that you can then export to PDF, and an inexpensive plugin for more complex impositions.
Since you've been using Print Booklet I'll presume that you just need 2-up, one signature, and no creep. If that's the case, and you have no content crossing the spine, this old script from Dave Saunders is still a champ: http://pdsassoc.com/downloads/Buildbooklet.zip. It creates a new file that's imposed which you then export as spreads.
If you have crossovers you'll need the newer version: Dave's CS3 Booklet Script which places your pages into a new file as imposed spreads that you export as single pages.
For more complex stuff, there's IDImposer: Overview | IDImposer