How do I prevent the image from shearing when I have an alpha channel?

I'm using After Effects to prepare some videos for the web. They are running at 320x240. The settings are Flv/F4v, Millions of colors, 15 FPS, RGB and Alpha, 44K/16bit Mpeg III audio, CBR 1 pass with a bit rate of 872, On2VP6 encoding.
I create the alpha channel from a greenscreen behind the actor using standard keylight and garbage mattes.
When I do not encode an alpha channel, the image is fine. My problem is that when I try to encode the alpha channel, the image shears to the left from bottom to top, and the whole image is transposed about 40% to the left. But we need the alpha channel.
This is what the shearing looks like. Any ideas on what is happening and how to prevent it? Thank you.

To check the clip, I made a small swf file the same dimensions and frame rate, 320x240 @15fps. It's a single frame, single layer with no skin. It just plays the flv file when you open up the swf. The flv file is external, so to test the results, I just keep rendering in AE to the same flv file name.
The first two seconds play okay. The shearing doesn't begin till after that. So I'm suspecting there is something strange with the keyframes. I even tried messing with the keyframe distance settings at 30 and 15, without effect.
The original video is an 854x480 mov file playing at 14.99 fps, millions of colors, Sorenson 3 coding. When I bring it into the comp, which is set at 320x240 @15 fps, I scale the movie to 50% in size. At your suggestion, I just tried making sure that all the frame rates are 14.99 instead of 15. Sadly, without any benefit. I'm still baffled.

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How do I prevent the image from shearing when I have an alpha channel?

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