I've noticed that the default rovers have it on the opposite side because the wheels go out slightly more on one side than the other, meaning one side doesn't get close enough. Look at rover from the side in lab and place the APXS on the end with the wheels closest to the chassis.

If its one of the small vertical rocks in the open, I had one of these problems(don't remember mission) and to get passed i moved around the rock to the other side and tried again and it worked.