My mod is nearly complete, I've successfully navmeshed over a huge area between several cells with non-trap doors, and trap doors both with no problems as of yet, and these are the same ID of trapdoors as the ones that work properly with NPCs so that's not it.. Then when I put a trapdoor into the bottom of a ship to teleport into an battle ring, suddenly NPCs refuse to use that door. Even with checkmarked green navmesh over the door. In other cells I've successfully made npcs take the trapdoor into the battle ring, and it worked fine, but for some reason this ship is being a major problem.

Any idea what's going on, and how I could fix it? Any idea why checkmarking the navmesh under the teleport marker makes it turn green, but it doesn't work right in this case?

Have you tried double clicking the green teleport markers and see where they teleport you to?