I don't see any problem with it.
In most of the pictures you're holding the IO shield in the wrong position. It is built to fit only in one position.
The IO Shield is fitted from inside the case, before you mount the MB. All your pictures are from outside the case.
Also pop the eSATA covers from it.
Take the MB out, test fit the IO shield on the ports directly, it WILL line up, then put the shield on the case, from INSIDE the case, then mount the MB again...