From reading your initial post, it sounds like you CAN control everything from within the software (manually), just that your timers have stopped working. That would point to an issue with the CM11A only, and not anything with your powerlines or signal strength.
Have you tried replacing the batteries in the CM11A, then clearing the interface and re-downloading (it has been a number of years since I used the original AH, so I don't remember the steps for that - sorry)?
Also, I know that with the newer CM15A, removing the batteris for a few minutes is all that is required to clear and reset it. I remember reading that they need to be out for longer (an hour, perhaps) to do the same for the CM11A?
Maybe someone here has more detail on that.