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Without seeing your source code I don't know if this is what's going on, but in the past I have seen this happen when I set variables using rospy.get_param() after I set up my dynamic reconfigure server. The reason for my problem is that I set my variables to values from the parameter server, thereby overwriting the variables I set earlier using the default dynamic reconfigure values. This has only been an issue when I have the same variable in my code set from both the parameter server and the dynamic reconfigure server.