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This looks like a difference between real time and simulation time. Simulation time starts at 0, so the difference between real time and simulation time is approximately real time, which is what you are seeing.
ROS uses simulation time, published on /clock, when the param use_sim_time is true. use_sim_time is set when launching gazebo. My hunch is that you need to launch the gazebo file first, then all subsequent files. See the ROS Time Docs for more information.
As for the message in the gazebo terminal regarding shutdown... I suspect that some node is being launched in both files. Look through the launch files, and I suspect there is one that you do not need to launch twice.
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