Same case I have. It's a good quality case, so I don't question the placement of the standoffs. What happens if you align the MB so that the standoffs match the MB? Does the IO shield then not fit at all?
1) Check that the i/o shield is pressed firmly in place along all sides. It takes quite a bit of pressure to do this.
2) Insert the motherboard so that the i/o shield openings match up with the motherboard rear panel attachments. Make certain that there are no tabs obstructing anything.
3) Press the motherboard into the i/o shield and line up the nearest matching standoff hole. It is easier if you happen to have three hands one to hold the case, one to push the mobo into the shield, and the third to put in the first screw. Do not tighten until all standoff screws are in place.
4) Once you get a second standoff screw in, you should be good.