Seems like what I did way back when I created the civ, was use the Terran Inverted palette as a starting point and then pick my own colours. Through a bit of trial and error, I managed to put together an XML mod which adds my custom palette.
The first hitch was that the default 'Diffuse Gradient' colour palette has a big ol' gap. Simply counting to where your desired colour is in-game won't work past a certain point. Opening up the palette in GIMP gave me a vague idea of which colour might match... nope, I was off by 3, but, hey, that's okay, fixed that. Similar story with the 'Light Gradient' palette.
Anyway, the second problem that I found was that the 'Surface Scale' and 'Surface Weight' didn't match what I originally picked out. After a bit of tedious in-game switching of palettes I found that the Terran Inverted palette matched except for the colours, so it must have been the one which I used as a base. So, I copied the values for that palette over and, sure enough, when I loaded up one last time, I had a 100% match.
Still have to pick out Painted Metal and Adamantium 01 when I go into the Ship Designer. But hey, progress.