I have exactly this same problem right now. I was doing MPEG streamclip, but that tossed the timecode etc, so I installed the canon mark iii plug in. The Transfer window comes up fine, and it sort of processes the file, but it never shows up in the Capture Scratch folder. And the completion circle is only half a moon.
Did you ever solve your problem? Can’t believe that Canon and FCP can’t work together, how hard can it be?