I have a clean install of KLAS 1.0, plus bleed fix above, and no other KLAS Afcads active. I too get the problem, it disappears when disabling "klas_papi_sa.bgl". Which appears to contain runways and flattens.
In addition to that, portions of the Afcad are visible through the ground textures. For example, near the taxiway M exit of runway 1L you can clearly see the gap between the apron polygon and itself. Removing all aprons fixes that, but then other things start appearing. Such as the hold short node markers (reduce taxiway link width) or runway links that cross the edge of the runway (reduce runway link width or place extra node on taxiway exit close to the runway). Does this have anything to do with texture transparency?