I started 12_5_2003_FS2_open_r with the -phreak parameter enabled, and weird things happened when I switched on wireframe HUD targeting. The models started to move in strange directions obscenely quickly (why is that destroyer traveling straight upward at over 500 m/s when it's not pointing in that direction? Why has it suddenly started moving backwards at a similar speed?) and then disappeared. That's right. You could still shoot them and otherwise interact with them, but you couldn't see them.
Is this why you used a command line parameter for PhReAk's stuff?