Please check four points.
1. Check that the encoder wires are running separate from other wires.
2. Check whether the encoder is tightly fitted in position. Dismantle and refit it again to check the integrity of the encoder and fixing plate. Sometimes if the fixing plate base is loose this can happen.
3. Check that the machine is in level, and that the nuts used for the rubber sound isolation pads aren't tight. These should be hand tight and shouldn't be compressing the rubber pads.
4. Check that the load switches come in correctly. If your load sensors have bottomed out, or if you have friction in the car frame and the cradle housing the switches, you can have improper feedback affecting ride quality.
I hope these simple actions resolve your problem. Kind Regards
P.S. I just read in your post that when you put load in the car the vibration disappears. Please check the first set of load switches, probably it is activating on empty car and giving feedback that the cabin is loaded when it is not, and when the load is introduced, it works correctly. I don't know whether you are using a strain guage or physical switches for each load. You will have to recalibrate the load switches accordingly based on the system in use.