There seems to be issues with heights. Place some waypoints and look at the waypoint height. It typically varies by quite a few meters (sometimes hundreds, sometimes fewer). If you assign those to TGT, your weapons will miss. If you correct the GPS height in the waypoint page using the height copied from that point on the map, you can correct this behaviour.
I don't know the definite answer, but if the algorithm that "paints" the target point doesn't have correct height data, the target point will be (for example) a hundred feet off the deck. If your weapons are headed for that point, they'll miss, proportionate to the variation between actual height and given height data.
The observations above concerning different maps and versions would support this. I'm sure these issues are to do with spot height mismatch.