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Did you switch chapters and play DA? There, where that option was first added, it was intended for use only on AI players, so it was disabled during the player customization stage of game creation.

Sorry to resurrect a dormant thread but I'm having this issue as well with the Ultimate edition. The Custom ship box is always greyed out. Strangely enough it was working at first, but i've no idea why it's stopped. I've only really been playing the TA chapter and when I have looked at the other chapters I've always set it back.

I've only had the game a coulpe of weeks so I imagine it's quite possible that I've changed an option somewhere.....what that might be I have no idea.

Any help would be welcome.

I think it's stupid that you can easily customize an opponent's ship style and have to do a bunch of text editing to do your own.  Come on Stardock.  Get off your butt.  You abandoned GalCiv 3 to support GalCiv 2, when are you going to fix this?  We shouldn't have to go through notepad to make our custom ship style apply to our custom race.  Seriously! 

Lets see some fixes already.

You don't need to use text editing. The point of the "custom ship style" is to make the AI use the custom designs. You can design your ships in play, and as long as you save them as templates, you'll be able to constantly reuse the basic design. I don't see the problem here.

Edit: You do need to mod in order to alter the designs of your starting ships, but you would need to do that with the custom ship style designer too.

If you just want to customise a ship style to use with the auto-designer (for example) what to do is to set your race as an opponent.  What this means is that the 'create custom ship style' button will not be greyed out.  Save the ship style with a new name once you're done making changes and then set your race as the player race again and choose the new ship style when you come to customise it.

But as qrtxian said, you still have to design your own ships either from scratch or by using the templates you've made, if you're not using the auto-designer.