Another interesting observation, that may help some people. I have lots of scanned .pdfs and for the "big ones", I use a feature in Adobe Acrobat 9 Professional that allows you to reduce the file size, presumably by stripping away alot off "unnecessary" stuff, by specifying a minimum version number for compatibility. By setting the version number high, such as to Acrobat 9, I can often reduce an 18MB file down to 3MB. However, once the reduction process is done, Repligo is completely unable to read the file (every page is empty with a big Red "X"), although the Library reader has no problems.
That's interesting. I wonder if it has something to do with Adobe's proprietary pdf formats. As I understand it, when they (Adobe) released the pdf format for non-proprietary use, they also created some pdf formats that remain proprietary to them (pdf/a, pdf/x, and there's another). The pdf/a is, I believe, a proprietary format used for their reader applications. That may explain why your altered files work on the Edge reader but not in the other program. It would be somewhat similar to why no one can create/edit TOC's, except with Adobe Acrobat software.