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I guess your node is using command line parameters but it is not ignoring additional, ros specific parameters.

While rosrun really just calls a binary and only passes the parameters you explicitly specify, roslaunch always adds the parameter __name to set the node name and maybe a few more. Topic remappings are also implemented using command line parameters. Make sure your node also accepts ros specific parameters or avoid command line parameters at all. Using the parameter server is a much better choice in most cases.