These are some screenshots from dyna-map however its the same case on rei's minimap.
http://gyazo.com/14003b3959a6bad82ad1f4d3303734ce
http://gyazo.com/0b0e54f2afa1cad39dee58250eb812ce
As you can see there are invisible blocks under the rails and depressions in the water from the invisible blocks.

By the way they are abyssal bricks, but it does this for every new brick.

Not my issue, I do nothing different from stone bricks.