I also have this problem with NavMesh and I'm on Linux too.
The way to reproduce is to have terrain with forest on map, than have NavMesh over 256x256.
If I open editor with such scene, everything is messed-up, I see lots of broken geometry on screen. If I decrease NavMesh size, the amount of broken geometry decreases and if NavMesh is under 256x256 it works fine. Looks like some corruption or type limits. I wanted to valgrind this, but had very little time for that. I don't know if NavMesh actually works when visually distorted, if I run in game mode bots behave the same.