I see that you use Acceleration, do you also use the option DX10 preview? if so, the reason why your strobe- and Nav light's don't show up, is because there is an bug in Acceleration/SP2 when using your lights under DX10 (also flickering textures on runway/taxiway crossings). Turning off DX10 preview restores normal operation of the lights. It's known, but wont be fixed  :-?