Try quitting the iBooks app, restart and then try to resume the downloads.
Go to the home screen first by tapping the home button. Quit/close open apps by double tapping the home button and the task bar will appear with all of you recent/open apps displayed at the bottom. Tap and hold down on any app icon until it begins to wiggle. Tap the minus sign in the upper left corner to close the apps. Restart the iPad. Restart the iPad by holding down on the sleep button until the red slider appears and then slide to shut off. To power up hold the sleep button until the Apple logo appears and let go of the button.
I like the double press ont he home button... I didnt realize that was even there... I quit everything and then restarted... went to ibooks and nothing was downloading.. I went to the store and pressed download again... but the books on the shelf still have black - non-moving progress bars...
any other ideas ?
Another thing that you can always try when downloads will not resume on your iPad is to finish them in iTunes on your computer.
Launch iTunes, and then go to Store>Check for Available Downloads from the menu at the top. Download the books and then sync the books to the iPad. When you perform the sync, make sure that you select the books to sync and make sure that you select the Sync Books heading as well in iTunes.