I had the radio on KMLE so it would be easy to start scanning at 88.1. I hit the button on my car radio every second or two and heard the tone(s) / announcement on every station except KUPD, KCDX and 105.9. (The radio skipped over AM 96.1 so I didn't hear them.) Is it possible that those 3 stations had aired the national test a few moments earlier or later than noon?
Two possibilities: the originating box from FEMA was set 3 minutes fast, so some brands of EAS boxes waited until 3 after the hour to forward the test. Also, with the cascading tones bleeding into the audio (FEMA was reportedly listening to the return feed from the PEP stations over the phone bridge and that bled into the outgoing message) some EAS boxes decoded the second set of headers and aborted the test.
FEMA wanted to see the weak points in the system. They found them.