I've started using hotkeynet and have noticed a similar thing. I DID have to do the hidden window thing, but that one is pretty obvious when it's the problem because the windows you run your rename script on won't be named correctly if hidden windows have sniped the proper names (unless you run the rename script twice then it's less obvious)

I honestly don't know what stops the broadcasting, but I HAVE noticed it only really happens if I tab out of a wow client (or sometimes into another wow client :/)

Also when it happens, I notice that if I bring up the hotkeynet window, any time I press a button it makes the windows notification sound as if I'm trying to click on something unavailable when a confirmation window is up... but I can't find any confirmation window. Let me know if you figure it out! I really like hotkeynet and find it easy to use so I'm really hoping that I can figure out how to fix it, and I'll let you know if I figure it out too.