Unfortunately, this is an Apple-caused issue (and it's probably intentional, due to copyright concerns).

Geeky background: Witch relies on the OS X Accessibility System to get information on open windows in other apps. Each window has a field (AXTitle) that contains the window title. Apple has left the AXTitle field blank, and without an AXTitle field value, Witch can't identify the window, hence, it can't list it.

Workaround: There's no complete fix, but you can get the iBooks icon back in the switcher, albeit without a window title. (You'll also get back any other app that you have running without open windows, so that could be an undesirable behavior ... but this is the only fix for now.)

To get at least the iBooks icon back, go to the Actions tab in Witch's settings panel, and check the "List apps without windows" option, and specify a placeholder. (For Witch 3, go to the Behaviors tab and enable "Show [something] for applications without windows" box, then pick an action.)

It doesn't really matter which placeholder you pick; here's how Help explains the various options there:

Check the List apps without windows option to, well, list apps that don't have windows in the switcher panel. There are three choices as to how those windows will be listed:

Bring to Front is the equivalent of choosing an app in the Command-Tab app switcher: The application will come to the foreground. If it has open windows, they'll be there. If it doesn't have any open windows, none will be opened.

Reopen (↺) is the same as clicking on an app's Dock icon: The application comes to the foreground, and if it doesn't have any open windows, one is opened. If the app has minimized windows, but no open windows, the most-recently-minimized window will be released from the Dock.

Finally, Both will give you the option of choosing either a bring to front or a relaunch action.