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I came across this same issue. rqt_plot saves whatever you last had displayed in a config file for "convenience" the next time that it is used. You can fix this one of two ways easily:

(1) Clear all topics prior to exiting

(2) launch rqt_plot using: rosrun rqt_plot rqt_plot -e (the -e option stands for 'empty')

Hope that helps. I found this very annoying myself.

Chief

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