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Have you checked your footage interpretation? With fields enabled, AE will indeed only show one field at any given time, reducing the effective vertical resolution. Also make sure to view your stuff at the full comp resolution, not half or whatever...
Open the clip in QT Pro and choose View > Actual Size, then save. Also check via Window > Movie Properties that the Video Track hasn't been resized. (Change it back and save it, if necessary.)
If you change the way QT views a file and save for any reason, that can affect how AE sees it.
I bet you are viewing your composition at "Half resolution."
Also, HDV is actually 1440x1080. QuickTime's Movie Inspector doesn't show you the actual size of the video, it shows meta data that can be really wrong, so it will often show HDV as just 1920x1080 because it is using PAR (Pixel Aspect Ratio) correction.
- Jonas Hummelstrand