I understand why you think it might be related to your Window Layout but it's not
Launching multiple instances is a function of your Character Set, filling into a Window Layout is just something they do after launching.
So first of all, 99% of the time this is reported -- especially with WoW -- the issue is the method of launching. You can launch a single instance of the game at a time through Inner Space by selecting a Game Profile through the Inner Space menu. If you do this, then in the upper left corner of the game window you should see both a FPS indicator, and a memory indicator. If you see the memory indicator, you launched the game through Inner Space and without ISBoxer, and that is why only one instance would have launched.
There are 3 ways you can launch your ISBoxer Character Set correctly (assuming you have Exported to Inner Space):
1. Right click Inner Space and, under the "ISBoxer Character Sets" submenu, select your Character Set
2. In the top left pane in ISBoxer, under Character Sets, right click your Character Set and select Launch
3. In the same menu as #2, there is an option "Create desktop launch shortcut". This makes an icon on your desktop to launch this team.
If that does not help, and the instance of WoW that opens does not have an FPS indicator or memory indicator or ISBoxer's Key Map and broadcasting toggle icons, then it's due to other software present on your PC interfering with Inner Space. If this is the case, go to the Help menu in ISBoxer and select "Diagnostics for game crashes", follow the instructions and after it "copies" the diagnostics, paste to privatepaste.com and give me the URL or paste ID