Where's Tom when you need him?
In the printing process, there a several different machines that paper must go though. All of these stages need to be adjusted, inked, registered (lined up), tested, and in this case, the tumblers on the number machine need to be aligned. When new ink is added to the press, sometimes you can "over-ink" the rollers, and it takes a number of sheets to evenly distribute it.
Before you run "good" sheets through the press, you run through sheets that you do not intend to ship. If there is waste from an earlier process, you use those sheets to get the next step "setup". Once these "setup" sheets have been used a number of times, they get destroyed. If you run out of "setup" sheets and you're not finished the setup, you then use "good" sheets and they become "setup" sheets and are suppose to be kept in a separate pile from the finished "good" sheets. You obviously don't want to destroy too much paper, but you also want to have a perfect print job.
Much discussion has gone on about how many steps there are and in what order they happen. The banknotes companies aren't talking.
That's what a "setup" sheet is.