Replace your lights section in your aircraft.cfg with this one. This is the default section and all the lights work as normal.

[LIGHTS]
//Types: 1=beacon, 2=strobe, 3=navigation, 4=cockpit, 5=landing
light.0 = 3, -39.00, -23.6, -0.25, fx_navredm ,
light.1 = 3, -39.00, 23.6, -0.25, fx_navgrem ,
light.2 = 3, -63.63, 0.00, 9.20, fx_navwhih ,
light.3 = 1, -37.00, 0.00, -2.59, fx_beaconb ,
light.4 = 2, -36.97, 0.00, -2.62, fx_strobeh ,
light.5 = 1, -63.05, 0.00, 9.75, fx_beaconh ,
light.6 = 5, -29.7, -1.3, -1.71, fx_landing ,
light.7 = 5, -29.7, 1.3, -1.71, fx_landing ,
light.8 = 4, -26.00, 0.00, 2.00, fx_vclighth,
light.9 = 4, -14.00, 0.00, 1.90, fx_vclighth,
Edit: The problem seems to be caused by the removal of the letter "h" at the end of the light effects name. I have discovered this problem on several of my planes now, and by simply adding the letter "h" to the end of the fx name it is fine again.