Found the problem. The second impulse was buried in the first impulse signal. I increased the audio level of the lower speaker and can now easily see it. All is working now.
I am running REW 5.20.9 on a Windows PC using miniDSP UMIK-2 microphone and a miniDSP HD10x10 box. I want to time align a two way speaker so I have placed the microphone 2.5 meters from the front of the speaker with the mike pointing at the mid position between the top HF horn and the bottom...