Thanks for the suggestion but unfortunately the problem persists for me. iBooks is unusable. There are probably a couple of dozen PDFs there and it seemed to be the last one "opened in iBooks" from webmail that triggered this.
This works for me. Actually after upgraded to 5.1.1, several problems occurred to my iPad, so I went down to the resotre mode and fresh my iPad with 5.1.1 fireware, re-installed all the software, and problem solved!