Your config looks okay I think? Did you remember to Export to Inner Space after setting your Hotkeys? Page Up/Down, right? Do the Ctrl+Alt+1 and Ctrl+Alt+2 hotkeys (which are configured per Slot in your Character Set) work?
Your Window Layout is not how this is typically configured but it should technically work. There's 2 things I might try that could help, less related to your ISBoxer configuration:
1. the development build of Inner Space (currently 5704 as of this post) has a positioning related fix, which could potentially be having some effect here.. To try it out (and revert back the same way later), right click Inner Space and select Patcher, check "Download development (test) patches" and then close and restart Inner Space to let it patch up.
2. the in-game video option for windowed mode/fullscreen/fullscreen windowed could potentially be causing a problem. you could try changing it to something that it is not currently, and see if you get different behavior. it's possible that one mode will work better than others for you -- definitely let me know if so
If those things don't help.. Usually in this scenario you need only 2 Regions, one for each of the two windows. You've got 3, where 2 of them are the same. There is nothing technically wrong with that, and again I see no reason why it wouldn't work (I mean, you just rearranged/sized the Regions after using the Wizard, right?).. but another option is to make the following changes to your Window Layout:
1. Delete Region 3 (right click, Remove region), so there are only Regions 1 and 2. same size, different screen
2. In the Slots tab (in the Window Layout Regions editor), set Slot 1's Home Region to <NO REGION> and Slot 2's Home Region to Region 2. (They will start out opposite)
3. In the Swap Groups tab, make sure Swap Group 1 under Roaming Slot says "Slot 1".
This will give you the same thing, except on 2 Regions instead of 3. But I don't think this will affect your Hotkeys, which look fine.
