Fortis1... Get Flicster Version 1.1.0.18 Product Version 1.01.0018 and that will correct your problems.
You did nothing wrong concerning your procedures... Maybe due to Flicster Version or some temporary Glitch.
Generally To make a New Palette: I am Using Paint Shop Pro 9
1. First change the Storyboards to 16 Million Colors.
2. Flood Fill the Frame Lines with Black , Flood Fill the Backgrounds with the Black 0,0,0,
3. Using the Rectangle Tool copy the entire Smaller Storyboards needed that have different colors (Ctrl+C) and Paste them onto the Default or Largest Storyboard with a Floating Image (Ctrl+Shift+E) so you can place the images without overlapping the other Storyboard images... left click to set and Right click to finish. (Note that you place the Background Color in the Background and Fill Properties Box so it will Not Copy when you Copy and Paste the Storyboards)
4. Remove (Change to Black 0,0,0) all Civ Colors, Background and Shadow Colors so only the Unit Colors Remain.
5. Reduce Colors to 160 Colors.
6.Open the 160 Color Palette (Shift+P) and Take a Screen Shot (Alt+Print Screen), Paste as New Image (Ctrl+V)
7. Save the 160 Color Palette Image as a .bmp for use to copy colors from for the New Palette... Use Pedit or what you prefer.
It will help you to make some Basic Unit Palettes: One that only has the Civ Colors, Smoke and Shadows Shades and One that has the Smoke and Shadow Shades with the Civ Colors Blocked Out (Top four Rows of Colors Changed to Pure Colors that are not used in most Units such as Pure Green, Red, Yellow, etc... These Palettes have all 160 Unit Color Slots empty = Black 0,0,0 so all you do is add the 160 Unit Colors to them when making a New Palette for a Unit.
You can make several Palettes to help you when Making Units such as Unit Palettes with All Smoke and Shadow Shades on them, Unit Palettes with Only Smoke Shades, Only Shadow Shades or Palettes with any changes that you might want to help you with various Types of Units.
Note: Using PSP, you will probably first need to save the Palettes as PSP Palettes then Change the extensions to .pal so they Open in Pedit.
Note that you can analyze the Jet Engine's Colors and add those Colors to the 16 Million Color Default Storyboard using a Large Square Brush size... about size 40. The Size will help keep those colors when you decrease Colors to 160 Colors because when we Reduce Colors the Colors are used based on the % of them compared to all colors needed for an image. IF any desired Colors are not seen when you reduce Colors to 160, go back and add the needed Colored Squares or make the ones you added Larger and reduce again.
Here is a procedure you can use for the Crisis Unit:
Combine the Run with Jet Engine Colors and Default Storyboard when making the Palette, You will need to use the extra
Non Civ Specific Colors that are in the top Four Rows of Colors for the Default, you will have an extra 30 colors and this Unit Needs those Colors.
Note: Using the Default Palette I Made, change the 160 Unit Colors to Pure Black 0,0,0 and save that Palette as something like Start Crisis Palette.bmp.
1. First Remove all of the 30 Remaining Colors that are on the Top Four Rows of the Default Storyboard by changing them to Pure Green then change the Default Storyboard to 16 million colors.
2. After analyzing the Colors you want for the Jet Engine Colors (I assume the Run Storyboard), save those few Jet Engine Colors temporarily as a .bmp image so you can add them to the Default Storyboard. (Those Colors can be the Same Civ Specific Colors of the Original if wanted and they will not be Civ Specific because those same colors will Not be in the Top Four Rows of the Civ Specific Colors on your New Palette).
3. Using the Default Storyboard, Flood Fill the Frame Lines with Black 0,0,0, Flood Fill the Background with the Black 0,0,0,
4. Remove (Change to Black 0,0,0) all Background and Shadow Shades so only the Unit Colors Remain. Normally you also Remove any Civ Specific Colors but in this case they are already Removed so change the Green Color to Black 0,0,0.
5. Reduce Colors to 160 Colors.
6.Open the 160 Color Palette (Shift+P) and Take a Screen Shot (Alt+Print Screen), Paste as New Image (Ctrl+V)
7. Save the 160 Color Palette Image (Crisis Colors) as a .bmp for use to copy colors from for the New Palette... Use Pedit or what you prefer.
8. In Pedit, Open your Start Crisis Palette and Fill in the 160 Unit Colors with your Saved Crisis Colors.bmp Image. Save that Palette for your Unit.
9. In PSP, Load Your New Palette to all of the Unit Storyboards
(Use Nearest Color Matching). Save those Storyboards.
10. Use Flicster to view the Storyboards and make the Finished Flcs.
Happy Modding 