Paul, I'm a little confused. You're zeroing the Y axis at the periphery of the end mill, then zeroing the X axis at a distance of 1/2 the diameter of the mill past the periphery?
You really should be using positive stops to locate the part on the table. This can be as simple as three dowel pins: Two to square the x axis and 1 to locate the Y. Or vice-versa.
Just remember to remove the dowels before machining