Technically you don't need it to be in the list, you can just type in the name, but I'm sure you realize that and need the convenience since you're making a lot of characters.

It should list every character that has saved information in any of the WoW folders configured for IS. If it's not being listed, I would probably check that first (e.g. the folder World of Warcraft\WTF\Account\MyServer\MyCharacter should exist). If you're using a different WoW folder for creating them, the "fix" might just be to add that to IS with Add Game (and then close IS for the change to save, then restart ISBoxer for it to load the change)