I'm creating 10 second 30fps 1920x1080 flash animations. I keep running into similar problems.
In one instance, CS3 crashes while importing a JPG sequence of 1920x1080 that lasts about 290 frames or so. I then used After Effects to turn this sequence into a SWF and upon importing it into flash the first hundred or so frames come out correctly while the rest appear as red boxes.
The same thing happened when I made an animation in After Effects, exported it to a SWF, and imported the SWF into Flash. It was also 1920x1080.
I also took the JPG sequence, turned it into a FLV, placed it in the scene with the FLVPlayback component, and when I tried to test my movie in flash, flash would crash.
Am I hitting a max file size with flash or something?