That is of course possible as well...I would think that this would require changing every AF2 file though....where changing the underlying texture simply affects a few files.
Runway10.bmp , runway13.bmp , runway 14.bmp and runway15.bmp are the grass, turf and gravel and sand textures if I remember that right, having just opened them...but the old noggin is a bit fried already.
Before going too much further I'd look at them in the main texture folder and see if any of them have white markings applied.
However if you suddenly have runway numbers everywhere I think your hunch with the AFCADs is probably the correct one.
Stefan