I used your window layout settings as best I could (everything but your massive region size... thats what she said?) and the feature worked correctly with both the dev and non-dev builds of Inner Space; I could mouse over any of the game windows, watch it focus as I moved, and type and/or click in the window without clicking or using a hotkey to focus it first.

It does only work if one of the game windows is currently in focus (i.e. if a browser window is focused, you will have to click or use a hotkey to focus a game window first)... but that doesn't sound like the problem you're having with it.

What version of Windows is this on? I'm currently testing on Vista (64-bit but that doesn't matter) but it should work equally well on XP or 7.