I dont know how you managed to do that, assuming you didn't like install an old version of WindowSnapper, or Zanthor's old scripts over ISBoxer.

It's entirely possible depending on your configuration that one or more windows might *start* in the wrong position (e.g. the main window moved to its small position). This is not a major problem and is solved by switching through each character. You can reduce the unpredictability at startup by using a window layout that uses "Region 2 is used for session 1" where the main window has its own inactive slot.

As far as the 3 windows loading instead of 6, are you using the wow launcher? or is this launching wow.exe? This would usually indicate that there's a second process launching when you launch the game that Inner Space is treating as another session.