Steps to repro:

1. Open attached project;
2. In the ProjectBrowser go to Assets -> Scenes folder;
3. Open 'Gameplay' scene;
4. Open Navigation tab (Window -> Navigation);
5. Click 'Bake' button;
6. Wait until NavMesh bakes and observe its surface.

Actual result:
Height leap artifact appears on NavMesh surface in area where Speedtree model is placed (see attached screenshot).

Expected result:
NavMesh should bake without height leaps, it's appearance surface should be consistent with terrain's surface.

Notes:
- Reproduces on both OSX 10.12 and Windows 10;
- Reproduced only once in a huge game project; was unable to repro in the new project;
- Reproduces in 5.5.0b7 and 5.5.0b8;
- Doesn't reproduce when SpeedTree are disabled on the terrain.