Media 100 can capture footage in 640×480 which transfers fine usually to FCP, HOWEVER, when you capture into Media 100 set to 720×486 (True DV) you are going to see that 6 line discrepency when you go to FCP which is 720×480. SO, outputting to DV then re-importing can work, but if you want to not drop quality you can render a movie export uncompressed (Quicktime, etc..) but go into settings and manually crop 6 lines of resolution off the picture so FCP will see it right.
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Bluerock Films, LLC
http://www.TGFILMS.com
7095 Hollywood Blvd #480
Los Angeles, CA 90028