ISBoxer/Innerspace works differently than keyclone. I had a similar issue to yours, there are a few things to remember.
Unlike keyclone, ISBoxer will render the other windows at the same resolution as the main, this is what allows for precise click broadcasting. This will give you a slight performance hit on your system.
Secondly, each character will have a seperate config.wtf file which would allow for custom graphics settings. If your main has graphics set to max then that will be the same for the slaves until you change it. This is what happened to me, essentially I had 5 wow clients running at 1920x1200 at max settings and got around 9-12fps. I then went it and tweaked the settings for the slaves, lowering the graphics to low and turning down shadows. I left view distance at the normal level. This is probably what your issue is. Check the graphic settings for the slaves.