I think the answer to this may lie with how you are turning on mouse and keyboard broadcasting.

Are you using the "Toggle" feature of IS or do you have it setup with an action to turn them on and a seperate action to turn them off?

I ran into what you are describing when I was using the toggle, I would toggle to all, but if for some reason one of them got out of sync, turning broadcast on and off would keep that one out of sync. By changing my keymap action to step 1 turning it on (all clients) and step 2 turning it off (all clients) I could easily manage this.

The only complaint I have about that now is that the steps don't stay synced between IS clients, so if I turn Mouse Broadcasting on in Client 5, switch to Client 1, mouse broadcasting is ON but I have to hit the mouse broadcast key twice to turn it off (it became second nature very quickly.)