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Here how I was able to fix the timestamp,

#include <pcl_conversions/pcl_conversions.h>
...
pcl_conversions::toPCL(ros::Time::now(), point_cloud_msg->header.stamp);

More information can be found here: https://answers.ros.org/question/172730/pcl-header-timestamp/ and http://wiki.ros.org/hydro/Migration#PCL