First, let me say that ST is a very good piece of software. However, I encounter the same problem again and again, even though I have upgraded ST on several times (I currently use the latest version. ST cuts off some pages, even before I reach the content selection step - it happens as early as deskewing.
EDIT: Nevermind, I figured it out. I had to turn off automatic mode in Step 2 - page splitting, choose the first of the three options and apply it to all pages.