Not all PDF's transfering to iPad 2 in sync

Hello all!
Today I downloaded a bunch of free magazines in PDF format on my laptop. When they were all downloaded I selected them all and dragged them into iTunes. I dropped them in the Books folder under the Library heading. All of the magazines show up in there when I click on books. I can even double click on them and read them on my laptop. When I plug in my iPad 2 and click on that, then click on the Books tab they all appear there under the Books heading as well. I have checked Sync Books, then All Books. Once the sync is complete only half of the books are on my iPad under iBooks (I have clicked on Collections and selected PDFs). When I go back to iTunes all the books are showing there. I have even tried changing the option to sync Selected Books, and then physically checking them all but that doesn't work either. So I went through the magazines that were on my iPad and unchecked them, leaving only the ones that didn't sync checked. When I re-synced it did put a few of the magazines that didn't sync last time, but not all of them. I tried checking All Books and syncing again and now I can't even get the ones I had on before back on. It's maddening! If anyone can help me figure out why not all magazines are going on to my iPad I would be so thankful! By the way I checked Newstand and they're not there either.
Thanks in advance!

Hi,
This is an unusual workflow, we have typeset the files in Tex. One of our client using XyVision. They have done the template in Xyvision, our requirement is we need to send full page as .eps with properly cropped, they will load the .eps into it and they will create PDF.
Here the problem is tex has links in some of the pages, when we saveas the file to .eps some links are there some were gone.
The Acrobat has compability to save the .eps with links we have checked and it is working for www.XXXXX etc.. but not working for SI Text etc..
We though that if Acrobat is capable of storing the links in .eps for www.XXX then why not for other. We would like to know the storage details how this links are storing.
Workflow is converting PDF full pages to .eps file with links, this .eps will be placed in xyvision then they will create the PDF so that the links will retain.
Shaji

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