I've looked everywhere for this answer and have found very little. What little I have found had to do with Windows, I'm on a Mac running Illustrator 5.5. This has bugged the crap out of me forever, how do I permanently add swatches to the swatch panel??? It's probably something really easy and I'm just missing it. PLEASE help.
Where did you save that document profile you edited? You should read this:
http://helpx.adobe.com/illustrator/kb/create-custom-new-document-profi le.html
I accomplish this by creating a custom swatch library. There are colors I often use. I put them all in there.
I then set it to be "Persistent". It's always there for me now.
Whether I raster image (which opens with a blank Swatch Panel), create a new doc or open an old one with it's Swatch Panel manually cleared.
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