@ScottMT,

I believe that there is a setting on some extenders when used in their normal mode that will reserve one of the bands for a high-speed connection, allowing a much better connection in terms of speed and latency.

Try Turning off the High-Speed Mode from your Extender Settings. From what you are describing you may have it set to automatically choose the bands and it is using the 2.4Ghz band for the "backhaul." 

Read More about the Feature in our FAQ: Configuring High-Speed Mode on Extenders

Otherwise, are you able to see the SSID of the 5Ghz and 2.4Ghz network when they are separated?