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You won't see the manifest files from the ContentLister. What happens after you open a new document for the first time is that the iLiad creates a directory with the same name, moves the document file into that directory, and then creates the manifest file/etc. The manifest (I think) is where it stores information like the last page. None of this is visible from the ContentLister, which will continue to show just the original filename, but you can get in and see it if you have shell access.
If it only happens on certain books, is there anything odd or unique about the filenames for those books? With Mobipocket, I think the filename and the book title are not necessarily the same thing. I'm not sure which one the ContentLister shows. Look at the Mobipocket file on your PC for a book that is having problems and see if there are any funny characters, spaces, symbols in the filename. Try changing the filename to something really simple, transfer the document to the iLiad again, and see if it makes any difference.
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