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Lance is right, if you shoot with a 1080i (interlaced) camera like, say, the Sony FX-1, you MUST deinterlace the footage at some point between the capture stage, or on the timeline in the edit stage or on export to your intermediate or final format if you want it to look good on a computer monitor.
I always deinterlace upon capture, edit and then export a full sized Cineform codec AVI from my hdv footage and then take that huge file into a full featured video encoding app like Cleaner XL or Sorenson Squeeze to encode it to the final formats and add the watermarks if necessary.
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