Could you post your hotkey file here (or email it to me) and tell me which key you are pressing when the running gets interrupted? Also which version of HKN are you using now? And are the windows still superimposed on each other exactly?

Edit:

that beeing the case is it possible to minimize a window and still broadcast to it without restoring?
That sort of thing varies from program to program. I don't know if it's possible with WoW. You just have to try SendWinM and SendWinMF and see.