The overall complexity of the vector determines the success. Are these spheres drawn using Flash? I'm able to easily draw a sphere on one frame, extend the timeline a bunch of frames, turn the timeline into a shape tween, add a keyframe at the end (which auto-adds the circle shape). I then delete the shape from the last frame and draw a completely different shape (15 sided polystar just to mention) and I messed with it a lot, moving points all over. I scrub the timeline and it morphes from the circle into the wacky polygon just fine.
If you haven't already can you try making your planet shapes in Flash and see if it works?
Lastly are you using 3d transforms on these layers? The double sphere almost looks like a cube has the sphere projected onto all sides in 3d.
Just open a new document and do as I did. Draw a basic shape using the built in tools, extend the timeline, convert to shape tween and then draw in some other crazy shape in a keyframe at the end. If that works, then reproduce your current issue using the AI files (which surely have more complicated vectors).
Import one AI file, extend out, shape tween, add a keyframe at the end and paste in a different AI document. See if you can reproduce the odd behavior. If it does then the vectors might need to be simplified. Simply the shapes themselves in AI and during exporting the file from AI use the lowest version of AI you can for maximum compatibility.
Well I just did it all in Flash. The red globe worked out a lot better but that orange one is repeating spheres again. It's better than it was, and good enough to turn in so I thank you for your help. I think I will revisit this, however, because I really wanted this scene to look good. It's a "bonus" to the project that I was going to put in if I got the rest of the scenes situated.
When you say use the lowest version of AI, do you mean the lowest available legacy save?
Yes the lowest version (legacy) supported in your AI's save dialog. The lower down you go the less features and bloat to the file. This can sometimes fix the issue. Also saving down to much less metadata-loving formats like EPS can help as well. The general idea is to simplify the file for Flash without losing the look as it will enhance your chance of successfully importing.
Let us what you end up doing. There's no shortage of animators out there using Flash for this stuff every day so any new bugs popping up are important to note in the bugbase.