I have had the exact same problem for the past few weeks. Started when IOS 6 came out. I can no longer open PDF attachments in either iBooks or in GoodReader. I could be IOS 6 came out.
Went to the genius bar at the downtown Portland Apple store. They didn't have a clue. Suggested I send in a bug report to Apple. Did that two weeks ago and have heard nothing.
Other threads suggest you could delete iBooks (and GoodReader) and reinstall them. Tried that. No good.
Until Apple sends an upgrade to fix this bug we're stuck.