Illustrator :: Remove Circular Shape From Rectangle - Smart Guide / Snap To Point Not Working

I am trying to remove a circular shape from a rectangle in illustrator, the retangles width is 10px and the diameter of the circle is 13px, I centre the circle ontop of the rectangle ( or I appear to)  but when I use the Shape mode tool minus front, the circle is no longer centred ( see images).

I have tried switching off smart guides and snap to grid and am still having the same problem.

In the above image you can see once I have divided the 13px circle from the rectangle it has moved off to one side.
 
Also when I am trying to manually place the circle ( rather than using the centre guides ) I can only move it by a large degree it alway moves further than I move the mouse, could this be because of a pixel grid? I do not think I am using this. ( can see in the above image where I am trying to place the circle and when I let go of the mouse, the grey circle is where it lands.
 
From the 2 images below you can see that there is a 1px difference on either side of the extracted circle I was trying to get centered.
 
I should mention that the 'Align to pixel grid' in the transform menu is inactive when I am trying to do this, as I initially thought that this may be the cause of my problems, but it made no difference.