Local Navmesh builder sometimes loses some geometry

Hi all,
I have 2 save games, and they have the same navmesh and local navmesh generation. However, if you load one, there appear to just be rectangles cut out of the navmesh. This doesn't seem to happen when playing the game through. It seems to happen after saving and loading the game, and only some save games are affected. Any ideas on what might be causing this?
This popped up yesterday after updating to 2018.2 so I wonder if it's a bug with that.

Thank you for any help you can give me.