I had similar problem in our IPCCX 4.0(5).

It has no problem if I start reactive debug in Script Editor. It happens to an IVR script. If I press an option within 4 seconds when prompt is playing, call will be treated as a direct call to the agent phone. CAD will change to Reserved and then quickly to Not Ready. When the call is completed, CAD will change to Ready immediately (Wrap-up time does not work). If I have only one level IVR, there is no problem. This only happens when there are two level IVRs (the same script for both of them). If I let the agent phone ring for 15 seconds (Call No Answer Timeout) then after 15 seconds, agent phone continue to ring, but CAD change to Reserved as it should be when receive an ACD call.

Fix: to switch from Layer 1 IVR to Layer 2 IVR, and from Layer 2 IVR to ACD, we use Call Redirect. We do not know what caused the problem. But when change the Call Redirect to Call Consulted Transfer, then the problem disappeared.