Apple has used the iBooks app in the past to detect if a user has a jailbroken iOS device. At launch, the app tries to run a bit of unsigned code. If it succeeds, the phone is jailbroken and the app quits, if it fails, the app opens normally. There have been fixes on Cydia in the past but I'm not sure if they have been updated for iBooks 2/ iTunes U. Find the developer of one of the original tweaks and write to them or just wait and see.