This happens when you have a vector shape in precomp and try to resize it.
Best thing is just Enable the "Collapse Transformation" switch of your comp and you will get what you want. Its for vector layers specially.
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[Dave LaRonde]"Glad there no video footage in it! It would have looked pretty grim. Although it worked this time, I recommend avoiding your solution in the future and going with Ted's suggestion."
Honestly, I'd recommend against designing for SD only altogether. Work in 4:3 safe 16:9, and you will be ready when the client (inevitably) asks for an HD version.
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I guess the advice on running that resize script would probably be the best advice in most cases. In my case, it was passing up some screwy masking issues from the sub-compositions, but I worked around it.
(I posted my process and also encourage following the tip for the resize script in case others have the same issue and need help.)