I have a very basic animation.
Bottom layer is a B&W version of a picture. Next layer up is the same picture in colour. Layer above it is a circle that moves away from the point of origin and back within 120 frames. It also gets bigger and smaller (at 60 frames, it is in the middle of the image and very large). I turn it into a mask before animating it (because if you don't do this in that order, masking just doesn't work- took me HOURS to figure that out), and everything looks good when I hit enter (test drive one clip in Flash CS4 - Windows): a small circular region in the bottom left is coloured, the rest is B&W, and for 60 frames this coloured region gets larger and moves to the centre of the image, and for the next 60 seconds, it shrinks back to its original size and position.

But when I watch it in SWF mode (control + Ente: "Test Movie"), all I see is the first layer, with no animation. What is puzzling, when I select "show redraw regions", you see this red box getting larger and moving just as my masking circle does. So it looks like something is happening, just the output is all screwed up.
Any ideas?