I also had this kind of problems, but my iPad1 is a 16gb. In my case, it appears to be a problem caused by low memory, or so it points out the crash logs the ipad is generating (eg, title LowMemory-2012-10-25-004434.log).
The crash happened with both PDFs and ePubs, but I could still use the smaller ones, and some I opened and after turning some pages, just crashed (and a similar log issued).
Since iBooks 2 worked fine, I decided to revert to that version. A member here, J. Jordan, helped me to install the previous versions. If you are interested in going that route you willl have to try and locate iBooks 2.1.1.ipa that might be somewhere in the Trash, iPad backups, or ~/Music/iTunes/iTumes Media/Mobile Applications.
Just be extra careful with your ebooks as it requires uninstalling iBooks 3.