Tilemap NavPolys are Garbled in a difficult form. How do I fix this?

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:bust_in_silhouette: Asked By AfterCadaver

I am producing a Tilemap based procedurally generated game. When it came time to test the navpolys I created in the tileset editor, the result ended up garbled. I placed a navpoly on the center tile.

Before I set update_bitmask_region() it the navpoly follows the tiles. after, the navpolys update into a garbled mess.

How do I fix this?