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I've seen problems like this in the past when I've had multiple nodes publishing to the cmd_vel topic; usually move_base and teleop. move_base was sending movement commands, while teleop was sending stop. This usually manifested as stutter rather than pulsing.

An easy check would to be rostopic echo cmd_vel and look at what commands are being sent. You could also use rxgraph to look at individual fields in cmd_vel.