Killing Carrier in Campaign

[LordArt 1]

I would first like to say that I'm greatly enjoying the game. Yes, there are a lot of crashes and reloads, but I can deal with that. My question is,

I just took the fulcrum island in campaign mode, and happened across the enemy carrier in the middle of the ocean almost immediately. After a lot of chasing (more like ramming) and losing a few mantas, I finally popped it with my plasma cannon. I get a message saying I won't be underestimated again. However, it doesn't seemed to acknowledge that I killed the carrier in the objectives, just that I now need to find technology that will help my walruses on wet terrain. So was that a fake carrier? A bug? Am I supposed to be hunting another one? Or at this point on, I'm just supposed to cap islands?

Yes, I played the original Carrier Command so I had a clue how to get the carrier, admittedly in the original 1988 version, the only way I could was with all 4 mantas with missiles and unloading and suiciding into it.

But in anycase, did I just break the campaign or can I continue? I mostly ask because I don't want to put all the hours in and find out that I can't complete the campaign because something was done out of order. Thanks!

UPDATE:

Well, as an update, I found the enemy carrier again, but it's a ghost ship. The AAs I destroyed on it before are still destroyed. You look at it cross eyed and it explodes (well, if your eyes have lasers, but it took as much as a gun emplacement to make it die again). It doesn't give me credit though. It keeps saying it's trying to capture my islands, but since it's a ghost, it can't do anything it seems, so I ignore it. I'm on the Aura in a box mission now. So I guess I complete the campaign then hunt down the ghost ship when the campaign script will allow it.

Any other ideas would be welcome.

Edited October 1, 2012 by LordArt
Further Information

[tharos 2]

*Spoiler*

You will get to fight it later. And yes it runs off everytime until the end

[kraxous 1]

Skrimish Spoiler:

Annoyingly in Skirmish mode, I think once you destroy it, it's just island capping from there.

[LordArt 1]

Well, I've killed it three times now. Although the last time it was fully repaired. I only started after it since it was capping my islands finally. I guess if left alone long enough it regens to full. A tomahawk seems to do enough to slow it down enough for the carrier to finish it off. I guess the campaign won't let it die until it says so. I hope the script still works when that time finally comes.