If you are under a transparent version of a roof, etc. it means you are behind it. I noticed one vase in the catacombs that my character opened from the opposite side of a low wall, but didn't have him going the wrong way for look. A few time when I had the alt key pressed he would head for a different pile of loot then what I was aiming for, though.
I have not heard of a miss-aligned auto map problem before, but the
patch couldn't hurt. Is it not updating properly, or is it centered in the wrong place?