ShiroKobbure,
The Army palette has 4 rows of colors for the flag in addition to the normal smoke and civ colors. This leaves 96 colors for the unit. Even if the unit doesn't have the multi-colored flag in the animation itself, those colors still have to be set. I used the Firaxis Army palette as a base, but the problem was that some of those flag colors were already in the unit. It would seem that either the palette colors need to change or the unit colors need to change. I think the challenge for Army units is that just as civ-color cannot appear anywhere in the original animation other than where you want it, the Army unit also cannot have any of those flag colors in the original animation except where you would want it.