Telemetry connection radio vs. hardwired

I have a Pixhawk and I'm trying to connect an Intel Edison SOC to it using Mavlink. If I connect using a 3DR radio, the connection works fine. If I hardwire the connection (serial port on Edison to Telem port on Pixhawk), I can read the telemetry data from the Pixhawk, but the Pixhawk seems to ignore any commands I send to it.

Any ideas as to why the Pixhawk is responding differently to a radio connection vs. a hardwired connection?

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