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Long story short, the mavros topics weren't publishing because there were firmware updates for the various radios in the system that we hadn't implemented. 1) The radio modem that connected to the computer was correct 2) The radio modem on the Pixhawk was out of date 3) The firmware on the Pixhawk itself was out of date

It's our first time working with the Pixhawk so we didn't think to check the firmware of various components, when we upgraded using the APM Mission Planner GUI then we started getting all topics being published correctly. Thanks to @vooon for his help.

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