No form of HD, including HDV ever requires the anamorphic checkbox to be checked, that's strictly for widescreen SD video.
You must be trying to use Quicktime Conversion rather Compressor, and that is your mistake. Compressor recognizes HDV properly as you can see from the inspector below. Then its just a matter of choosing one of the two IPod/IPhone presets from the Apple Devices directory and it encodes 16x9 every time.
David Roth Weiss
Director/Editor/Colorist
David Weiss Productions, Inc.
Los Angeles
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A forum host of Creative COW's Apple Final Cut Pro, Business & Marketing, Indie Film & Documentary, and Film History & Appreciations forums.
