I'm working with linux here, so all the Direct Show stuff doesn't apply. But the responses from you both have pointed me down the right path.
From what I can tell, there is nothing wrong with the encoded video. The problem is with the players which do not correctly display anamorphic subtitles. It was with VLC that I noticed this. But what I did find was that mplayer is displaying them correctly. I may file a bug with VLC.
Thanks for your help.
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