ok, let's go through the isboxer settings again.

1. Screen sizes
When you create your windows layouts, you define the screens and their sizes.
Click on a Window layout, then in the bottom frame click on regions and for each screen (green rectangle) you'll get a "size" parameter.
This parameter must be of the same RATIO.
For example, since i have mine on 1344x840 on the main, and 336x210 on the slaves (4x smaller)
you don't have to use those numbers obviously (my screen setup is a bit special as this is my second computer, not the main) but the ration must be maintained.
All my screens have a ration of 1.6, and are set like that to match the main screen (on the other computer) at 1680x1050 (still 1.6 ratio)

2. Rendering sizes
in my 2-computer setup i had to change the default resolution in ISBoxer to match the main screen.
The resolution drop down can be found in the lower panel, when you click on the name of your layout (top item in the treeview)
You'll see the switcher keys settings and all that, and towards the bottom you'll see a checkbox with "Desired rendering size". Make sure this is set correcty.
I personaly have mine set to 1680x1050 (you can type the values if they are not in the list) to match my main resolution on all wow screens.

hopefully that'll help
make sure you save your ISBoxer settings and then export them to Innerspace (use the ISBoxer file menu)