Hi rom, when you export with n-gons, there aren't any triangles stored in the file. The receiving application will generate its own triangulation of the n-gon, or with FBX it's possible to use triangulation from the FBX library code which is what tends to make FBX have more uniform behavior.

I wonder if your render engine and current settings are particularly sensitive to skinny triangles.

Does your renderer use raytraced shadows? What happens if you turn that off, do the darkest spots go away?

- Michael