I just realised that the Dorsal Anti-Collision Beacons were supposed to be light red, and not the 'normal' red that I had been setting them. Judging by which ships have light red beacons and which ones don't, I guess I forgot somewhere between starting the Commando class and finishing the Commando class 8 months later.
D'oh!
Fixed.

Changed colour of cockpit light - I just noticed that it was the wrong shade of purple. XD