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No idea. I'm simply not doing enough with Flash to be of much use here. On a guess I would think that maybe it hinges on some script, the layer state or the keyframe range of the animation being misinterpreted, just impossible to diagnose. Can you provide the SWF for testing along with a snapshot of the Flash timeline or the open FLA file?
Here's a note from the "Supported import formats" section of After Effects Help that seems relevant:
"Interactive content and scripted animation are not retained. Animation defined by keyframes in the main, top-level movie is retained."
If you want an animation in a SWF to be retained when the SWF is imported into After Effects, the animation must be keyframe-based (not scripted), and the animation must be in the top-level timeline (not nested).
I may be late but better late then...
You can nest hundreds of layers as long as all symbols are graphics.
People try to use a Movie symbol and this is script executed.
I am animator on cartoon all done in flash and we have dozens or more NESTS!!!!
Eyes inside of head inside of Character in car on stage...
Trick to not crashing is in FLASH
Set publish settings to FLASH 8.
Never use FLASH 9 with Actionsscript 3... This adds a lot of instability.
1 of these swfs in a project could kill it.
I render SWF at 30fps at 1920x1080 then into AE, then scale down to SD wide screen resolution 720x480 16x9.. set scale to 45.5 x 44.5 percent.
I output final animation at Quicktime ANIMATION 100 millions of colors... 1.21 (16x9)audio added at 48k
I have hundreds of hours trying to make this work reliably and finally I got the mix.
Then I take QT to Premiere for final edit, audio and titles.