isboxer not detect the screen resolution or do I have to put that in some where ?
Yes ISBoxer gets the information about your monitors from Windows. Usually this is pretty obvious when you use the Quick Setup Wizard and get to the page where you pick your Window Layout style

Assuming that's what you did, AND that you didn't change your monitors around since then (e.g. by adjusting their resolution, etc), then you may need to change a setting in the game rather than in ISBoxer. Specifically I would be looking at the Windowed Mode setting in the game, if it's set to Fixed Windowed it may end up sizing wrong.
If you can't access this setting with ISBoxer up, then you may need to reset or manually edit your core_public__.yaml files. There is the main file and one per ISBoxer Character. To reset, delete the per-Character ones and either rename or delete the main core_public__.yaml file. The per-Character ones are created with the settings from the main file, so note that if your main file is set exactly like this still then the next time you make new Characters in ISBoxer, they will have to be fixed as well. If you're manually editing the files, then the line I believe you're looking for says something like...
- Code:
FixedWindow: [130398053149194431, false]
If that says true, it might break the windows.
