Low brightness setting doesn't "stick" in iBooks
On the off chance you weren't already aware, you can modify the system-wide brightness by double-tapping the home button and swiping the "shelf" to the left.

iBooks can set a lower brightness than the system will allow outside the application -- so if you frequently set it lower than the system's lowest setting, you'll have to make that change every time you open the app.  As you can see in the screenshot below, when the iPad is at it's lowest system brightness, the iBooks brightness bar is at about 20%.