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What format are most of the books?
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In order of frequency: pdf, palm doc, mobi, html and word.
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Are you using a network drive? That is known to be slow.
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No.
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That is because calibre is trying to get the metadata for the PDF. To make things go faster, goto: preferences -> plugins -> metadata reader, and disable the PDF plugin. Everything should go much more smooth.
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I tried that, and also tried disabling the PDF metadata writer (since my troubles are on write, not read). Neither made a positive difference.