If you open the color palette (when for example adjusting the color coding of keywords or labels) and you click on ‘Add to custom colors’, it overwrites the last custom color you already added instead of making a new custom color.
This only happens right after you opened the color palette the first. If you then start adding more custom colors they (apart from the first) get added as expected.
If you then close the color palette and open it again, again the first color you add overwrites an existing one, instead of adding.
You can actually drag the custom color you create into the color box of your choice! And you can rearrange the other colors by the same method, for a total of 16 custom colors.
Surprisingly, the technique does not work in Paint’s or WordPad’s rendition of this standard color control, even under Windows 8. But it works splendidly in Scrivener.
– Jerome
oh nice! Thanks for the tip. I hadn’t even thought of trying that 
That is even better than a workaround.