Did some testing and there's two things that can cause that.
- The Walkable area is inside-out. This could happen if you dragged the points out so the ones at the bottom originally are now at the top (or same for right/left). The easiest fix is to re-do the area (add another walkable area and delete the original). Edit: Just added something to check for this and handle it, so in later versions it won't be a problem
- You have a "hole" that's blocking off a whole section of walkable area. This is on my todo list to fix. I do have an alternative way of blocking a section, so if you need to do this, let me know.