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setMaxVelocityScalingFactor(..) is a MoveIt function that influences the eventual time-parameterisation of the path.
It does not directly influence fanuc_driver_exp (or any other robot driver for that matter).
What it does do is change the maximum velocity that should appear in the trajectory that is the result of the time-parameterisation of the path.
Now whether a receiving driver is able to faithfully execute that trajectory is something else entirely, and for fanuc_driver_exp there is even a note in the readme about this (from here):
tries to adhere to commanded velocity constraints on trajectory segments (but will most likely fail)
Having said that, a very slow trajectory should result in slower execution, even if the driver will not be able to actually execute the trajectory completely as it is specified.
If you can provide two wireshark captures of traffic between your ROS pc and the controller (one with a regular trajectory and another when you've used setMaxVelocityScalingFactor(..)) we can see whether at least all the infrastructure on the ROS side is functioning correctly.
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