This seems to be the issue:
Cedar Point listed their distance in their submission from the highest point to the intersection of the two runways at the airport, which is 19215.51 ft, or 3.16 nautical miles. The FAA determined the distance to be 17,907 ft, or 2.94 nm from the closest endpoint of either runway.
Oh, and in case you were wondering what the 3 nautical mile radius is from the point the FAA used:
And relative to the highest point of the coaster as shown by CP: