The cursor centering in the other wow windows is new (broken recently) and I noticed it in the past, but I didn't notice it today and IS got an update this morning so maybe its fixed.

There is an option somewhere (sorry, cba looking it up) to turn off "switch master on focus" that you are experiencing. I had the same problem and managed to turn it off; check to make sure ISBoxer isn't sending a command / keypress when you switch windows. Make sure something like "Only when I press hotkey" on window switch is checked as well. Just done this typing all from memory, but if you have a good look in ISBoxer's options you should be able to sort it.