Made an HTML5 flash doc consisting of people popping up over several frames to show a crowd. The images came from a Photoshop PSD file with preference set so that separate layers would be kept. But only one image of the nine pops up-- other people are invisibile. Type, on another layer, works fine. Some of the images are symbols, some not. Moving layer order foreground to background doens't help.
Here's an image of my stage & timeline. When I publish, only one of the nine people's heads shows up.
there used to be (and may still be) a limit to the number of alpha bitmaps that can be layered.
delete 1/2 those bitmap layers and test. if everything shows up, undo that delete and delete the other 1/2 of the bitmap layers.
if everything shows up, you can convert those bitmaps to vectors (modify>bitmap>trace bitmap) in flash and they'll all show up.
What I did was export layers from PHotoshop and import them separately as individual images. That worked.