To be clear, I've never seen this happen so we have no guaranteed fix. Here's everything that comes to mind...
No luck on either. The same problem persists.

This is a pretty quick and short negative response to what should have fixed the problem, so my first assumption is that you didn't fully understand what MiRai said, and the game is probably still loading the same EVE configuration as before.
So my question is... when MiRai said this..
You can try changing your display modes associated with each client. Since you can't really edit your options at the moment on those small screens, the easiest way to do this would be to delete all of the virualized files that ISBoxer creates, then log into the game solo w/o Inner Space, set it to the display mode you want to use (I assume EVE should be using Fullscreen mode), exit the client, re-export from ISBoxer so that the new display mode is copied from the main file to the others, and then see if that changes anything.
... What did you actually do? Do you know where EVE keeps its configuration files? Which files did you delete? What setting did you change, and what is it set to now?
Here's what needs to be done...
1. In
C:\Users\<USER NAME>\AppData\Local\CCP\EVE\c_program_files_(x86)_ccp_eve_tranquility\settings, delete all of the
core_public__-<CHARACTER NAME>.yaml files. They will be re-created when you launch the game through ISBoxer, by copying the main core_public__.yaml file.
2. Open the game normally, while those files are deleted, and change the Fullscreen/Windowed mode setting from whatever it is now, to something it isn't now. Either Fullscreen or Windowed, definitely not Fixed Window.
3. Make sure it saves the setting, then close out the game and launch your team with ISBoxer
As far as switching from dx11 to dx9, I would have expected a "how the hell do I do that". Because there's no setting in the game to change this, only the launcher, and it only has an effect when you use the launcher instead of launching the client directly. Are you using the EVE launcher when you launch your team? Or are you skipping the launcher and launching the client directly? If you're launching directly, you need to edit your Game Profile (
http://isboxer.com/wiki/Game_Profile) and in the Parameters box put "
/triPlatform=dx9" (with no quotes).
If none of that works, there's probably something else on your PC interfering (apparently blocking the resize when ISBoxer wants to move and resize the window), and it might help to have "Diagnostics for game crashes" from ISBoxer's Help menu (
http://isboxer.com/wiki/Diagnostics) to help narrow that down...