II'm having an issue as well. im exporting swf files out of flash cs6, and then importing them into AE cs6. all the frames of the swf files are visible and play properly one day, and then are gone the next (literally - walk away from my computer at 6, don't shut down, back at 9:00) - running only two frames, or showing no images at all (blank frames)
running cs6 with all updates on Mac OS 10.7
no error messages, opened AE and the swf files are wrong. ive previewed the swf files through the flash stand alone player (v11) and they are wrong there, too (only two frames or blank). Previewed files through web browser (safari, chrome, and opra) still incorrect.
i was was able to import swf files into AE with no problems a few months ago. There have been no changes to my system since then.
graphics card is AMD Radeon HD 6970M 2048 MB, system has 16 GB RAM
no third party software, running only flash and AE and safari, open GL is irrelevant (problem persists in stand alone flash player) turned off render multiple frames, turned off cache, turned of XML number on import settings, exported in a legacy player from flash (8), updated flash player (only for browsers, no updates to stand alone player).
Hopefully THAT is enough information to get some help.
I'm having the exact same problem. Flash files won't draw in the window when rasterized. Says the file is damaged... Re-exporting the .swf doesn't work. Trashing prefs works temporarily.