Did Inner Space detect your WoW automatically, or did you use "Add Game" from the IS menu? Unless Inner Space is pointing to something other than wow.exe (like a launcher) then ISBoxer should be offering to fix any problem it sees in your Config.WTF file, which should cover any known reason why you'd only get 1 WoW window and it'd be in full screen mode.

So assuming you're not telling it No, I don't know why you'd get that if you used the Quick Setup Wizard and didn't make any other changes. The only other thing is if you installed ISBoxer to a different location than you installed Inner Space, then your ISBoxer folder will have a Scripts folder, with scripts in it that need to go into the Scripts folder for Inner Space. Without them ISBoxer will not function properly