Actually, I just entered the Stagnant Tunnels, and it looks like I just circled around with the boat, but I haven't explored in detail since I still see black fog across most of the map. So, that's not the explanation unfortunately.
Here is a link to pictures: http://imgur.com/vnl1u6F
I'm just really curious, and if anyone can explain this, it would be fantastic. I'm just starting to understand the game, so I really didn't know what was going on in the beginning when I was clicking on things.