Mike: now you tell me!
I find it easier to work with them all as a single file anyways, but that might just be me.
This is the last time I bump this thread I promise. I had a go at JJJ's data as well for something to do. I tried processing it straight from the avi, then centered using ppm, then centered and split into RGB. The centered/RGB'd one ended up turning out the best and is below.
http://thinksays.com/img/jjjupiter_rgb_final.jpg