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.

Updated from pre-1.0:
Added CPU extenders; Added 2k Cargo & 250 Ammo 'Weights & Volumes' containers; Added Shield and Warp Drive; lengthened by 1 block, change of some shapes, rearranged some devices.

Changed the shade of green used on the Starboard illuminated Orientation Panel because the lighter green that I was using was indistinguishable from yellow when next a yellow Ventral illuminated Orientation Panel.

Repainted and retextured whole ship.

Mistakes were made. Shhhhhh.

Texture changes - specifically a decision change regarding which textures should be used for floor and ceiling that includes illumination. Plus replacing the old "vent" textures which has changed to no-longer have vents to one that has a grill and replaced texture on Orientation Panels.