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Try deleting the bookmark/annotations files (\MyDocuments\Annotations\*.ebo).
This seemed to help performance, especially with a large volume I often used as reference.
Keeping most books on SD, I'd just remove the *.lit when I was finished. I never bothered to go through the official "remove from Library" process in MSReader. Lot's of obsolete files out there and I suspect they were "plugging up the works".
Just note what page you're on if your still reading the book!
Still, MSReader is much slower that previous version.
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