Well the truth is, I dont know how to Gif it out of flash because of what you said. The colors gets messed up. I use another program called Easy Gif Animator. If your planning to download that, Heres what you need to do;
Once your done with your Animated Gif, You need to go to file and Export -> Export Movie. Make sure the file Image is PNG. From there, It should be easy putting them all together. If you have figure out some other way to animate, Its your choice.