Tile Handler Helper script seems to malfunction after the following happens.
Create Recast graph area. Create a Tile Handler Helper in scene as well.
Start the scene, have code generate a level for you and re-scan the graph, start using navmesh cutting scripts.
The issue seems to lie in the order of execution.
Scene start (generate grid on awake) with Tile Handler Helper in place, and then adding objects and rescanning - Breaks
Scene start (no generate grid on awake), adding objects by code, re-scan and then adding TileHandlerHelper by code - navmesh cutting works fine.