So I put a "repeater off to all other windows" action in with the step to toggle repeater on.
To be more correct you'd actually want a Mapped Key Step Action to set the Repeater Toggle to Step 2, followed by a Do Mapped Key Action to do the Repeater Toggle -- this makes sure the icon and Shift+Alt+R hotkey are in the correct state, so you don't have to click/press it 2-3 times to turn on Broadcasting Mode when you go back to that window that had it on.
But am I missing a case where one might actually want it on in more than one window at a time?
I cannot think of one.
Uh, sure. Don't forget there are people doing things with ISBoxer that you're not doing, and therefore are probably doing and thinking of things that would suck for you, but are good for them.
Playing a game like Diablo 3, Broadcasting Mode is typically on by default, and the toggle affects all windows at a time instead of just one. So if you play 4 instances of D3, you probably want it on in all windows. Switch to another window, you want it in the same state so you can continue combat, etc.
Playing a game like WoW, it's off by default and the toggle affects only one window at a time. Turning on broadcasting mode is fairly rare. Some people would prefer it turn itself off when you switch windows, and get confused that it's still on in that window when they switch back. Entirely possible to set that up. But the way it is designed you can be broadcasting something (e.g. clicking through quest windows), quickly switch to the one window that isn't in the right spot and move it (or click on the right quest option, etc), and switch back to the broadcasting window to continue where you left off.