I been trying to find a few pictures and I read the install instructions. It looks like the way you attach the mount to the tailgate might change the height. They suggest the 2 bolts to the passenger side, not sure why, but maybe they have a reason. I don't have a mount and can't find any really good pictures, but it looks like if you flip the mount so the 2 bolts are to the drivers side (like it is sitting in the picture), it might raise the tire. I wonder if the guys here that have no problem, if that is the way your mount is.
If you guys can take a picture of your spare tires and post them here, we might see if there is a difference. Just a thought.
PS: I could be completely wrong on this, I'm just going but what I can see mostly in the attached picture.