Calibre doesn't view pdfs natively - it attempts to convert them to an ebook before displaying them. Many pdfs don't convert very well, as you've just discovered. You can configure Calibre to launch an external pdf viewer instead under the preferences.
As far as documents being listed and not having actual files - there have been some bugs in past releases where this has happened - changes have been made over time to reduce the chance of it happening, and hopefully it's fixed, but no one has been able to come up with reproduction steps to verify 100%.
Last edited by ldolse; 01-12-2011 at 10:14 AM.