ISboxer will set it's positioning based on the Window Layout region sizes, not what you set the game to, which should match the RESET region size for each swap group, and is normally going to be the large region for that swap group.

But you have three ways to resolve it.
1. Set the RESET region for Swap Group 2 (the Swap Groups Tab there on the right), to be Region 1. So then all the games will be rendering at the same resolution (that's what the RESET region does).
2. Create a new region for Swap Group 2, which is the same size as the RESET region for Swap Group 1 (if swap group 1 has no reset region, then the size of Region 1 is what you want). You don't have to assign it as a home window or anything. Just purely needs to be there for sizing purposes.
3. Under Repeater Profiles -> Default, set the Mouse Cursor Postioning Mode to be one of the Scaled options. Although you are better off with options 1 or 2, because otherwise your game UI scale changes so things can end up positioned slightly differently.