I am getting CK warnings when I open my mod, that Cells I have navmeshed and finalized and have verified as working in the game with the beta need to be refinalized.
OK, when I check the navmesh for the cells it mentions - no errors.
I do the find edges, and cover step - no problems.
I finalize yet again - no problems - all cell borders are green.

Yet I am getting CTD at some of these cell borders in game - and I am noticing NPCs having problems freely traversing modded cells and stopping at the borders.

Anyone else noting odd NPC behavior?

Hmmm, so far all my navmesh is working fine. What exactly are the errors saying? I get errors for 'reversed normals' and such things which can be hard to track down, but nothing that causes CTD's or severe issues.

It is telling me that the Navmesh in Cell (-3,6) and does this a total of 7 times for other cells I have modified.
Whe I go to those cells, there is nothing wrong with them and after I re-finalize ( check navmesh, check cover, finalize) the cell boundaries are all green.
In game, NPCs seem to be lost and not crossing over the cell boundaries. At certain edges I get a CTD.
These are vanilla cells that have been modified.

AV: aren't your cells new cells? Mine are Vanilla that have been modified (forts added, etc.)

are you using .esp or .esm as this can make a lot of difference to how navmesh works out...

.esp
Didn't have a problem until the 9th of June.

Let me try a new game and see what happens.

I reset some of the adventurer and traveller mods I was using so they are moving again.
I kind of use them as a test of whether NPCs can freely use the navmesh and cross cells.

This was a Vanilla Mesh Skyrim - my mod un-checked. That is my base line.

Next step - see how they move on my cells that have been altered / enhanced.

I haven't been having any trouble with the navmeshes I'm building for Open Cities. NPCs are navigating them just fine in Riften and Markarth. Not done with Whiterun yet though.

Thanks, Arthmoor!
Once I got my test NPCs moving around, with a new game; and tried with the altered navmesh in the known good 0.0.0 beta version of my Mod, all seems OK. I did find a repeatable CTD spot on the hill just to the NE of the bridge between Ft. Greymoor and Redoran's Retreat. But that is not a Cell I altered.

I do thank all who responded.

This is a very complicated game and there are so many moving pieces. It is hard to figure out the real cause of observed issues sometimes.

I'm also getting a number of messages telling me that several (5) cells need the navimesh re-finalized. Message says that the cell is missing navimesh bounds. (whatever that is). I go through all the steps and finalize it and after saving and going back in I get the same messages over again. None of my NPCs are having problems crossing cell boundries though. Is there some way to make this stop?

Sounds like you might have done what I did in one cell I finalized. The vanilla navmesh in one of the buildings I connected a door to was split - there are actually 4 navmesh islands inside the cell instead of one complete one. I proceeded to combine them. That resulted in one navmesh that worked, and 3 more that wound up as deleted records. It's the deleted ones that are raising the complaint.

Of course, deleted records are a source of crashes for the game, so I'll have to remember to undo this and find a way to fix the problem while at the same time not destroying the existing data. Probably easiest to pick one of the 4 and repair it while simply dragging the rest out of the mesh boundaries and leaving them alone.

I am getting the same exact issue as Arion. However, I hesitate to call it an issue because I just ignore it and it doesn't have any effect on play. Heck - even my horse follows me all over the fortification if I forget to park her in the stables.

Athmoor: How do you detect the Navmesh islands? I wonder if my two-story towers which are half on on a seam - connected 1st story to 2nd by stairwell on cell seam are registering as islands, even though they are connected with green borders.

I do have a mysterious CTD issue about 10 cells away, though in a vanilla cell I have no edits in!! I will open a new topic on it, though.

The CK will identify any navmeshes it sees as islands. That means they have no connection to any other accessible navmeshes in the area. This isn't always bad though, because you can have a corner of a cell on a cliff that has no connection to the ground and that hasn't been finalized to connect to another cell yet.

Or interiors with split levels and no connection between them other than a jump link.

If you have an interior cell though that's all one piece and it looks like they're all supposed to be connected but still list as islands, it's probably a situation like what happened in the Warmaidens shop in Whiterun. Someone at Bethesda didn't notice that they'd put down vertices that weren't connected to the remainder of the navmesh and it resulted in two large sections that don't connect to each other. The NPCs can't navigate over this and end up unable to reach their upstairs area.

Whiterun actually has a couple of other problem cells like this too but the isolated triangles are all in out of the way spaces I decided not to touch.

What about floors that connect via another cell?
1st floor and 2nd floor on cell one; stairwell connecting them in cell two. cell borders green ; Npc travel normal .

If you have load doors connecting them and those navmeshes have been finalized, they won't show up as islands.

These are exterior cells.

also note the dev response on the bounds issue on another thread by that topic .