Hi Agama, thanks for the quick reply. I think you may have misunderstood my post though. If you open a PDF on Acrobat you can number the pages however you like. These numbers are embedded in the pdf. They need not correspond to the actual position of the page. So the 8th page might be numbered 'xiii' and the ninth page might be '1'. On the kindle, the page number displayed for a pdf would be 'page xiii' followed by 'page 1'. On the sony reader, my PDFs seem to display 'page 8' followed by 'page 9'. In other words, it ignores the embedded page numbers. The problem is that the table of contents in a book obviously lists the page numbers as printed, which correspond to the embedded numbers. If I enter the page number to navigate to on the Sony Reader I get to the wrong page because it ignores the embedded numbers. This does not occur with proper bookmarks, but these are not present in many of the scanned documents that I use.
As for converting to ePub, I have had little success. I have found the reflow option on the PRS T2 to be far superior to the results of converted epubs.