The purpose of the custom ship style button is to put together a package of templates out of those you've created, so you can tell the AI which designs to use as a base for its ships (you'll note that it is available only when customizing an opponent); it's not actaully intended to apply to the player's ships. If you'd like to adapt it for player use, there is a stickied thread on the subject over in the modding category of the forums.
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