If you have iOS 4.2 you can force the app to quit. Double-click the 'Home' button to open up the multi-task bar at the bottom of the screen. This shows the apps that are currently running. Press *and hold* any app icon until they all start to 'jiggle'. The jiggling app icons will all have a 'cross' in their upper left hand side. Press briefly the iBooks app icon on the cross and this will force it to quit. (Note this does not delete the app, but just forces it to quit). To quit the multi-task bar hit the Home button once. Now open up iBooks again and see if you experience the same problem.
If that doesn't work have you tried 'restarting' the iPad? Holding down the 'power/sleep' button for about 3 seconds will power the iPad down completely. You'll see an icon of a rotating 'bezel' appear in the middle of the blank iPad screen once the power-down starts. When that bezel disappears, power the iPad on again. This time the Apple logo will appear in the middle of the screen for several seconds as the iPad powers up.