I think I have the solution, first, make sure the areas are a little below the surface, then go to tools, Navigation mesh,then click on select all,then collect geometry, this will take a while, depending on how many areas you have, then when finished click on Generate Navigation Mesh. Save and test it, that should fix that.
Remember to click on select all, or else it wont work.
Good luck!
Remember to click on select all, or else it wont work.
Good luck!
Hmm, the problem might be with the Select All, forgot about it when made the rest of path areas and went through the whole process, gonna re-make them (deleted them lol) and now hope I won't forget about Select All 
Edit: That was, still, random invisible walls there and there, even if overlap it's still not read as one big brush in game, the whole concept making primitive cubes for navigation is a bit...turn off.
Edit: That was, still, random invisible walls there and there, even if overlap it's still not read as one big brush in game, the whole concept making primitive cubes for navigation is a bit...turn off.
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Well I have experienced that issue only once, and I think i solved it by making the Areas smaller, when they are too big the are buggier, to check if your area is too big just put a mesh with collision, if you can go through it, it means your area is too big. I also hate the PathArea system.