I have had similar problem with a very small number of PDFs. In the beta 2.0 release, most documents turn in a second, but I have a few that are taking between 5 and 10 seconds per page turn. iRex staff asked me to send them a sample document a week or two ago, which I did, and they said they have repeated the problem and are investigating a solution. So, all you can do is wait for the official release of 2.0 of the software from iRex, and see if they have been successful with the speed-up.
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