Stymied by X-rays

Here is an animation I made last week for the MIT/HHMI video series for undergraduates. In this video, a professor describes her work in X-ray crystallography, and in doing so explains the principles of light wave diffraction. That is where I come in. I make these animations in Flash, but create many of the images in Illustrator. Here I'm apparently approaching the limits of this strategy. These waves of X-rays brought in from Illustrator don't obey the timeline, but rather appear only when they are good and ready. Luckily the person who assembles this into the video can control the timing, but that's not an ideal solution. I'm still deciding what is the best way around this without compromising the quality of the images, probably by rasterizing or flattening the transparency, but in the background I am hearing the call of 3D animation software growing louder and louder.