I originally had a level, fully navmeshed, that worked perfectly. Later I added a new area to the level, in the same cell, that was only accessible through a teleporting door connection. So, I was left with two separate navmeshes in one cell. My followers seem to work just fine, but I am having issues when enabling NPCs, who seem to want to lump up together in the new separate navmesh. At the moment, I only have one NPC who gets stuck there. Do islands like this break NPC pathing?

Yes, islands break it from what I know, it needs to be consistent. They can't island hop.

Yeah... figured as much. Soon as I deleted it, everything was fixed.

I have to question why they were there at all though. None of their packages and none of my quest scripts tell any of them to go there, yet ALL of my NPCs end up stuck there. You'd think they could just ignore the island...

I'm also having a similar issue with my mannequins now. I deleted the island navmesh, and now my NPCs are all getting stuck where I have a mannequin that is disabled (along with the markerheading and the trigger box being disabled). Any ideas? I don't really need those mannequins, but it is still annoying since it just started happening.

Also, Colbert is awesome!

If an NPC doesn't have specific AI or scripting to prevent 'wandering', they will usually show up in navMesh at higher altitudes. Is your modded area an interior or exterior? If an exterior, it sounds like you're afflicted by NavMeshBug... and would probably have to wait until it's fixed by Ma Beth (hopefully in the upcoming v1.6 final release), depending on exactly what your NPCs do and where they travel. If an interior, and your NPCs all have proper AI, and all your navMesh is properly created and finalized... then I'm not sure what it would be.

I've only seen islands cause problems in Vanilla cells (Tamriel worldSpace); and should be avoided in those cases until the Bug is fixed (though this island thing may be a separate bug/issue, but we'll see soon enough). But I have plenty of interior islands that I never have problems with.

To fix wandering mannequins (and/or any NPC that doesn't have proper AI): it has to be linked to a ref (xMark, a static, idleMark, whatever); then in the script you have to force it back to that ref in the onCellAttach event (moveto, transTo, whatever). Mannequins have other issues as well (nakedness, item duping), so you may want to look into my Vanilla Mannequin Script Fix. It's GNU licensed so you can either implement it into your mod, or just link to it on your site... if using it (or a variation of it), you must rename the PEX to something unique, so your mod won't conflict with Vanilla (should someone want to use an alternative script for Vanilla 'quins).

By NPCs not having proper AI... they may have perfectly valid packages; but if it's all conditional and those conditions aren't met, they will not have 'valid' AI and will wander. Also, I believe sandboxing falls into the wandering category if not linked to a ref.

VanMannScriptFix
http://skyrim.nexusmods.com/downloads/file.php?id=10652

[EDIT: I DO have islands in Vanilla Tamriel worldSpace that work; but I also have had problems elsewhere.. so it seems this issue depends on the location and seems to be arbitrary. Backup your data and give it a try... given you have the AI stuff above under control.]