whe I fire it up only one window appears
How are you firing it up exactly? (What are you clicking on?)
The classic newbie mistake is to right click Inner Space and find the Diablo 3 sub-menu and select Diablo 3 Default Profile. This launches the game with Inner Space, but would be completely unrelated to your ISBoxer configuration. If you're launching the game with its usual launch shortcut on your desktop, that's just going to launch the game without Inner Space or ISBoxer altogether.
The right way to do it is to right click IS and, under the ISBoxer Character Sets sub-menu, select your Character Set.
Then, if only one window is coming up, the real questions I have are:
1. Is there an FPS indicator in the upper left corner of the window?\
2. Is there a Memory indicator in the upper left corner of the window, directly below the FPS indicator?
And, finally, when ISBoxer is launching your team it will produce output to the main Inner Space console: http://isboxer.com/wiki/Console
and this information can be useful to you or me in further diagnosing the problem