I also ran into a horrible "Waiting for Acceptance" problem that had a different cause, but the basic trigger was the same: the controller sends a discovery response to an AP and never hears back.
It sounds like in your case, the controller itself dropped its own discovery response. In my case, the controller sent the discovery response with a bogus source IP address (tracked it down to an obscure controller bug).
But I think in general, "waiting for acceptance" happens the first time the controller sent a discovery packet to the AP (it seems even if another part of the controller code dropped it) and doesn't hear back. I don't ever want to see THAT again!
noemi