Can you temporarily configure all motor exactly the same and see if that makes any difference? What about if you cut the max speed and accel params in half. Do the motors still sound rough?
Try swapping the wiring for a motor that runs well with a motor that doesn't. For example, if the motor on pins 2 & 3 runs smooth, and the motor on pins 4 & 5 runs rough, take the wires from pins 2 & 3 and connect them to 3 & 4, and the wired from 3 & 4 and connect them to 2 & 3. Does the motor that originally ran smooth (when on pins 2&3) still running smooth (now that it is on pins 4&5)? If the issue stays with the same motor, then the issue is probably with the motor driver and/or wiring from the motor driver to the motor. If the issue stays with the same pins on the PMDX-414, there may be an issue with the PMDX board.
You can also post your profile here, or list the motor tuning values for each motor if you don't want to post your full profile.
