It does show the 4 holes, that is the blue lines, I am presuming they are drill holes rather than milled circles?
Regarding the code, it is the way the circles are done, they are using G1's rather than G2's and thus each complete circle in your code is made up of hundreds of short moves rather than just a single G2.
That is likely a function of your post processor in that it is outputting straight lines instead of arcs.
Hood