You need to correct the palette of the flicster storyboard
before you paste you rendered pics over it. The first and last rows in the palette of a flicster sb are used for civ colors, transparency and shadows. So if your unit is rendered with some colors that are in these slots the palette gets messed up.
The following I wrote at the CDG about it (ignore the parts you already know
):
Finally the Civ-colors. First in your 3d software create a material for the civ color, pure red or blue is recommended, but theoretically any other color is possible. It depends a bit from what is already in use on your plane - if the pane has to be blue in Civ (like those US WWII Navy fighters) you cannot use blue as civ color. Basically, the civ color should be used only as civ color. So on a blue plane make some parts red for this purpose. To get the civ colors displayed correctly needs however a bit more work:
First, you need a Flicster 8bit storyboard. The easiest way is to load a Firaxis plane into Flicster, then save it as PCX storyboard with the needed size and frame number (same as your 24bit storyboard generated by SBB has). Now load that 8bit PCX storyboard pic into an image processing software like Photoshop or PSP and open its palette. Please see now the attached pic, it shows a palette in Photoshop from the storyboard of my SeaHarrier.
The color row at the bottom is in red tones - this is the civcolor (please note that in some gfx software this row appears as first, not as last). You see that nowhere else in the pallette there are red tones - this would cause trouble. So if you used red as civ color while rendering, but red is not the civ color in your 8bit storyboard, edited the palette so that you have your red tones in the last row, and nowhere else (Photoshop lets you create automatically several color tones row if you define a start end color as dark and light red).
The upper row is in magenta tones, the first (or, in other case tha last) color is the background color. Since we defined the ground as pure magenta it should also be magenta here. This color will be transparent in the game. The other, darker magenta tones in that row are needed for the shadow. Again, if your 8bit storyboard looks different, edited the palette to have the magenta row.
Aside from civ-color and bg/shadows, I named the first and last four rows "critical slots". This means they are not only used for shadows, but also for various other effects, so it means that these 8 rows should not contain any colors that should be seen unchanged on the plane in the game. Means if your plane should have a green-brown camo pattern, all green and brown tones should not be in the first 4, or in the last four rows. If they are, edit the palette, if it is done, save the entire PCX storyboard, now with corrected palette.
(Please note: if you cannot create most of those tones automatically like in Photoshop, palette editing can be a real pain. In that case you could try to use the palette from one of Firaxis units, eg. when you save the Firaxis bomber as Flicster 8bit PCX storyboard, you get a palette for a plane in dark green camo. However, you probably would have still to adjust civ color and shadow colors).
So, finally you have one 8bit PCX storyboard with your own palette, and a series of BMP 24 bit pics for each direction, and each anim. Now use SBB to generate a 24bit BMP storyboard by SBB frome your series of single pics. Load the storyboard into you image software, copy it, and paste it over the 8bit PCX storyboard you created (turn any special color reduction algorythms which may create dithered or grainy pics off, if possible). Since you corrected the palette before, the 24bit pic should adapt the colors of the 8bit PCX storyboard easily. Now save this again, and load it into Flicster to test how it looks - if all looks good (including transparency and civ colors), save it as Flc unit anim.
