If your math for the X axis steps per inch is correct... then I would guess that your X axis acceleration is set too low. Here's information I received from one of the 'guru's' with regard to acceleration when I was setting up my machine...
The acceleration setting effects how the steppers stop or decelerate. An acceleration setting that is to low will cause coasting down of the axis and the machine to overshoot where it should have stopped. It can also cause the machine to overrun home or limit switches. A general rule is to use between 10% and 15% of the velocity as a starting set point for the acceleration setting. A good visual indication would be to snap "rapidly release" an axis jog key during a jog... that axis should stop motion instantly.
It sounds to me you have the Y axis accel set in the correct range but your X axis accel is set too low and you are consistently coasting down and overshooting that 1/16".
Senna
aka BOOMER52 >>> http://www.rcgroups.com/forums/member.php?u=159693