First off, if you got the new ISBoxer 38 but did not get the new Inner Space build with it, update Inner Space. If you launched it today you'd probably notice an update for it as well, so I'm guessing that's not the issue for you.

Secondly, if you got both ISBoxer and Inner Space updated, but you did not do a fresh Export of your ISBoxer configuration, you will need to do that now.

If you've done both of these things, and are still having an issue, then it sounds related to a bug I have solved in a test build and am pushing live soon. The bug being that if you have multiple monitors, and the game launches MAXIMIZED (many games have an option for this) then ISBoxer doesn't seem to swap correctly (typically described as "the game is on the wrong monitor"). This has come up more often recently due to ISBoxer's new window layouts for multiple monitors This can be fixed by un-maximizing the game and restarting.

If you can't find that option or you'd like to see if my test fix works for you, come by the ISBoxer Chat Room and I'll give you a link.