Ok, that's just plain weird.
Here are some random things I'd try if it were happening to me.
At the bottom of most the iBook Store screens you can see your Apple ID, or Sign On. Make sure you are singed in. You might even try signing out then in again. Just tap the button.
Close and restart the app. With the app closed, double tap on the Home button to get the multitask bar. Tap and hold on any icon until they start to jiggle and the minus sign appears at the top left. Tap this to close the iBooks app. Tap the Home button again, relaunch the iBooks app and try again.
Restart: Hold down the power button until the power off slider appears. Slide it off. When the iPad finishes shutting down, hold down the power button again until the Apple logo appears.
Reset: Hold down the power and home buttons until the Apple logo appears. The iPad will reboot. This usually takes a bit longer than a restart.
The last thing to try is to delete and re-download the iBooks app. If you have all your iBooks synced to iTunes it should not be a problem to get them back quickly. If you don't use iTunes you can still get them back by downloading them from the store again. The exception is PDF files. PDFs that you've added directly to iBooks on the iPad will need to be saved somewhere so you can load them again. You can email them to yourself if nothing else. If you added PDF files through iTunes, you will be able to sync them again.
If none of that works, I don't know.
