Hi, I know I'm not the person who originally asked this question, but I have been having the same problem. Thank you for taking the time to post your solutions to this site. You have helped many other people by doing this.
I do have prizmo. But I like KNFB for this work. As I got both apps, I like doing it with knfb reader.
I've found this a couple of times. KNFB does OCR very well, but the pages are sometimes out of order. Anyone else had this problem? I can't tell whether it's something to do with the PDF or not. I emailed KNFB support and got a curious reply: first sentence said 'we will pass this on to the engineers.' second sentence said 'I hope this information has resolved your query.' Is it just me, or does the second sentence not really follow from the first?