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My guess is that the controller in move_base that is generating cmd_vel has a hard time to find the right control commands. This controller basically takes the odometry message and tries to follow the planned path as close as possible. Verify that your odometry message actually makes sense, in particular the velocity values are important for move_base. Check that they actually match the actual velocities of your robot. Be sure that velocities are actually sent in the robot's base frame, not in the odometry frame. I.e. when the robot is driving straight forward with 1 m/s x velocity should be exactly 1 and y zero, no matter in which direction the robot is moving in the odometry frame. Try plotting the velocities with rxplot, drive forward, turn 90 degrees and drive forward again. Both times, only the x velocity must be 1.