If you are changing from one color previously obtained by feeds to another color, you may also be hitting thresholds by where the points combos you are attempting push over or under a value in the RGB.
As in, if you had previous changed to a color X, you might have been at the very edge of one or more of the RGB values required to achieve that color, as in if a value needed was 150, but you actually had hit 154, but that was still enough to be within the correct color range. By then changing those value by a second combo of feed aka "set RGB values", it may can cause those "at the edge" values to then not work out correctly in the math which then pushes it into a different RGB color. Like, if you need to increase the 150 value by 25 and not exceed 176, so you feed 25, but you were at 154 to start, so 154+25=179 which is 3 over the 176 max, so now the color is different.

It is best to feed the Chocobo the "reset" food first, allow its color to reset to the default, then change the values from there.