1. All character sprites have to share the same palette
2. You must have a sprite 0.0
3. SFF must be in this order (top is first, bottom is last) 9000.0 (Doesn't need to share character palette) [can either be here at the end of the character sprites] 9000.1 (Doesn't need to share character palette) [can either be here at the end of the character sprites] 0.0 all other character sprites (sharing the same palette) any other sprites (can have any palette not shared with character sprites)
4. When saving SFF do not allow it to auto-organize the file (this can change where the sprites are placed, and cause the break of the palette)
By this you can see that the palette fix may be different for each broken character.
Commonly I am fixing number 1 above. I find that a lot of spriters will get half way through spriting the character, and change the palette they are using (same colors, just different placement on the palette). This causes the "break" in the palettes as they only work to change colors when the colors are placed in the same spots on the palette)
That all being said Fighter Factory has some tools built in that make changing the palette within the SFF file easy, but has to be done for each character sprite that does not match the character palette. This can be easy if there are only a few sprites not matching the palette, but then there ones that can be harder with 50% or more of the sprites that need to be fixed.
Here are a couple quick ways to fix this right within fighter factory.
Part 1 shows how to set the palette back to default for the sprite if they are already sharing the palette but simply a different palette using "Apply the current palette to the specified sprites"
Part 1
Part 2 shows how to set the palette back to default if the sprites are not sharing the same palette using "Advanced Palette Editor"
Part 2
As you can see by "Part 2" example the sprites are also not sharing the same transparency color either. You can load a sprite in the right hand pane of the advanced palette editor and copy over the default transparency color before "adapting the image to match the color of sprites"
Part 3 shows how to add different colors to an existing palette using "Advanced Palette Editor"
You need to have saved a sprite from the SFF with the correct color in it to use to copy the color from in Advanced Palette Editor.
Part 3
As you can see you can quickly fix most common issues caused during creation all within Fighter Factory.
Fighter Factory 3 and Studio were used for the videos.
If it hasn't been fixed by the time I get home from work tonight I will have a look and get it back to you tonight (probably in about 5 hours from now).
If you have a good backup of the files this should work for you.
*.BAK files are normally the actual original file with a .BAK at the end (instead of .CNS, .DEF, .CMD, .SFF etc) Windows does this to create a copy of the file (instead of overwriting the file).
You should be able to simply change the file extension and the file should work (alternately the files other than the SFF should open with notepad).
There is a great free online audio converter tool, you can upload, adjust the volume and download it back right away. It works great for smaller audio files (I just ran a bunch of Killer instinct voice clips through it as they were also too quiet and they sound fantastic in MUGEN now)
Michael with updated sprites is almost ready to play. I also am doing a minor color separation on him so he can have palettes (about 50% complete color separation).