John
the problem you are seeing is referred to as being out of TRAM. This is where your spindle is not perfectly perpendicular with your waste board. It really shows up when you use a large diameter cutter. If you see the washboard effect in the Y axis direction the the spindle is tilted clock wise or counter clock wise when looking at the spindle from the front of the machine.
If you make the cuts using the X axis and see wash boarding then the spindle is tilted clock wise or counter clock wise when looking down the rails of the X axis.
The standard way to check this is to put a dial indicator on an arm in the spindle and rotate it around. You will see your reading change as you turn it around. when you can turn the indicator a full 360 degree with out seeing more than a couple of thou difference then your spindle is then in TRAM.
Hope this helps
Dave