I don't know what's wrong. Navigation, map and root are all in 0,0,0
Can you take a picture of your complete navigation mesh?
Also, note that navigation has been rewritten from scratch in the master branch (which will become 4.0 in the future). It's much more capable there.
here's a picture of generated navmesh. I tried all 3 generator types, tried changing agent size to much higher than should be. I even tried making my own simple navmesh, and it's always wrong. Path wants to go into the wall out of navmesh and then proceed with "drunken" way, wobbling from side to side and often missing hallways by few meters and going in the wall/air.
Thank you for telling about master branch.
I for some reason had 0.9 scale in my Navigation node. I changed it to 1.0 and at least now navigation is walkable, it's just not optimal.