TIm,
I do not think that the JVC HDV codec has been implemented into FCP5.0 yet. I know that the codec is different from the SONY HDV codec, The sony deck does not play beck the JVC format and vice versa (so much for having one format?)
So I think that you are actually trying to do somethign that is not possible.
Maybe you could create a capture preset that matches the frame size of the JVC HD as it is recorded on the tape. I am pretty sure it is a 720P HDV format.
David