As you can see in the pictures the cell border runs directly under the house and shed on the side. I am not sure what to do in this situation as obviously I don't want any navmeshes under the house, yet I do need them running along the exterior deck of the house. This is the vanilla navmesh, I haven't altered it yet....

http://i110.photobucket.com/albums/n99/Shezrie/nacprob1.jpg

http://i110.photobucket.com/albums/n99/Shezrie/nacprob2.jpg

Does the cell border need to be defined on every single edge of the cell? After all, no NPCs will be crossing the cell border through the actual house mesh. Is it safe to simply delete all the navmeshes under the house leaving no border under there?

Thanks for the help!

Delete the tri's under the house [or the ones you don't want NPC's getting too] then rebuiled the navmesh to include your additions. Personally, I would move the house so it sits inside one cell and doesn't cross several like you have it. Although that won't make any difference in the game [mostly], it would mean you'll end up spending less time navmeshing all those separate cells and aligning the border verts.

The cell navmesh border really only needs to be defined where edges [verts] meet at the border and overlap. If they are not, NPC's won't be able to cross over those tri's and with isolated tri's spanning two navmeshes [or more] like that it will cause some pathing hiccups. The CK might also throw an error at you that some edge borders aren't aligned or connected. Generally speaking, it's always a good idea to connect them - if you don't want to, don't put tris there.