It could be any number of things.
Tuning:
First pull the motors away from the rack and run a problem program and see if the motors sound good and give smooth movments.
Rack and pinion:
The pinion needs to be square to the rack, and the rack needs to be level. If all of this is perfect, you may need a little more pressure pushing the pinion into the rack. On mine the spring was a little weak and the pinion would walk out of the rack and cause shaking. The problem here is your rack is coarse, and will require more pressure to keep the pinion seated, and more pressure will suck up more power. Are you sure the pressure angle is the same on you rack and pinion?
Gantry:
You don't make any mention of your motor config, so I will go with 1 on each axis. Is the shaking worse far away from the motor on the shaking axis? If it is you probably have a rigitity problem.
Motors:
Are you using servos or steppers? If you are using servos you will need to gear down the pinion. If you have steppers, with 200ppr you are moving your gantry about .018" per step, which is pretty coarse, and could be giving you some issues.
Good luck.
On all equipment there are 2 levers...
Lever "A", and Lever F'in "B"