I don't think the Windows command prompt has ever used the traditional CGA colours on a VGA or later display. The traditional CGA colours are
these ones (000000, 0000aa, 00aa00, 00aaaa, aa0000, aa00aa, aa5500, aaaaaa, 555555, 5555ff, 55ff55, 55ffff, ff5555, ff55ff, ffff55 and ffffff). The Windows system colours were tweaked to simplify the dithering algorithm giving
these much uglier ones (with the lower contrast between the dark colours and black) and reordered to 000000, 800000, 008000, 808000, 000080, 800080, 008080, c0c0c0, 808080, ff0000, 00ff00, ffff00, 0000ff, ff00ff, 00ffff, ffffff. So, in the sense that the colour scheme is based on the 8 corners of the RGB cube plus one bit for a "bright" level, nothing changes with this update except that the exact set of colours has been chosen by a designer rather than a coder.
Anybody know why IBM picked the colours it did for CGA in the 5153 monitor? Trixter
hinted that it comes from one of the IBM 3270 series of terminals, but it doesn't seem to be the original
3279, the first colour device in the series (according to
https://en.wikipedia.org/wiki/IBM_3279 this only displayed red, green, blue and white) but perhaps it was the later model that could do 7 colours (though I'd have expected one of those 7 to be yellow and not brown).