Here's an issue I've been having with InDesign using "print booklet". We do a lot of books where the cover is color, and the inside is black and white. We set the job up in single pages, but use print booklet to print them in printer's spreads. Usually works fine if you send the entire document. But, if you try to send individual pages (like page 1 and 40 of a 40 page book), it prints them separately with a blank page next to them.
What I normally do is take the front and back cover and put them into a document by themsleves and set it up print size. Then run the inside of the book using print booklet in single color, and just delete the cover from the RIP before it's imaged.