[Suicide Junkie]

If you right-click the ship, you should see that the Organic Armor components are intact before the weapon hits and gets a negative damage display.
Once the weapon hits, SE4 calculates the change in hitpoints since the Last hit, and comes up with a negative number.

In any case, the overall effect during combat is the same.
After combat, it is different: If the ship takes damage, but then does not get hit for the rest of the combat, the OA components WILL be repaired, even though the damage report display may read 500/1500.

I am absolutely sure of this in SE4 v1.49.
I tested this in SE4 v1.64 (Gold), but you are probably using v1.60.

Since my CD just came in yesterday, I'll set it up and check for you tonight.