Try resetting you iPad to get iBooks working again. Press and hold the power button and the home button together for at least ten seconds, until the Apple logo appears.
After resetting your iPad take a look at iBooks and see if it's working properly. If not, try re-syncing with iTunes once or twice, that seems to have resolved the issue for others. If it still doesn't work you should contact Apple. They have first-class customer assistance and should be able to get things sorted out.