Honestly, try using standard AIC files but render them with a solid color as a lower layer that comes through the alpha. Then you can use the transparent color FX and dial in the color. I have a hundred plus pieces of content I am using on a show now which I have done this way and they work fine.

Just FYI, I had a few pieces with some foliage which was green and blue so I made by background layer red and was able to make the background only transparent which looked great.

I wouldn't suggest the animation codec unless you are only running very few layers. If this isn't an issue then Simon is right.