Huh...
Umm...
I don't think your issue is related to any ISBoxer or Inner Space updates (which by the way were December 27th, and 21st, respectively), I don't see what different SLI modes have to do with window switching in the first place, and your Window Layout (at least according to your pasted configuration) doesn't include swapping behavior anyway. On top of that, I can't personally test 2x2 SLI.

What does come to mind is that you have Focus follows mouse enabled. This is pretty much expected for your layout and shouldn't be a problem. The Focus follows mouse option should only be available when swapping features are disabled (and again, your swapping is disabled), but I've seen someone manage to turn it on
with swapping, which would definitely cause this issue if you've found a way to do that. What would happen with both swapping enabled AND focus follows mouse is you put your mouse over one of the small game windows, and it activates, moving to a different spot on the screen while your mouse cursor stays in the same location; then your mouse cursor is over another window entirely, so THAT window moves to the main area. This would be expected to happen until moving the mouse cursor over the main area.
That's the only known reason for the issue you're describing, but from the configuration you've pasted I'd say it shouldn't happen. You can disable this option to rule it out as the cause though. I would want a fresh paste with whatever changes you've gone through to be sure, I guess.
The only other thing I see regarding your profile is that you've got MMO - Standard and MMO - Pro configuration styles from the Quick Setup, neither of which are really useful for EVE Online. Next time through I would definitely go with what is selected by default for EVE which is "Minimal". This wouldn't really be a big problem, but you've got some wires crossed with your Key Maps. Several individual Characters have Key Maps assigned that probably should not be, and some of them specifically have two custom-named versions of "Always On" enabled at the same time, PLUS the main "Always On" which is assigned to all of your Character Sets. So on 5 out of your 6 teams, pressing one of the toggles in almost any window will do the toggle 3 times instead of 1 time. Luckily you've only got "Next window" assigned a Hotkey in ONE of those, so we can assume this isn't the issue you're running into.
I would probably recommend starting again with a cleared profile. You can keep this profile backed up, just go to File and use Save As. Then go to File and select Clear and let it clear out your entire configuration. Use the QSW and leave it at Minimal setup. You should get an "Always On" Key Map and that's it. You shouldn't need a different version of it for each Character Set or anything. If you use exactly the same Character Set and Character names when setting it up, then any Video FX and such you've configured within the game will still be there. Just don't forget the option "Video FX Viewers stay when in background" when doing your dxNothing part again
