I'm transcoding the red r3d files with the log and transfer window to apple pro res 422 and sometimes I'm finding it's only take a portion of a clip. I then have to recapture the extra part of the clip. This is getting annoying.
I am not sure what could be causing your issue. Perhaps, are you reviewing at the files in FCP while you are dong the import? This has cause truncation of 7D footage for me so I stopped and just let the machine do its thing and dont touch it any more and have not had this issue again.
Also, Have you tried Red Rushes? It trans-codes beautifully. I just did 7 hours worth trans-coding to 1080 ProResHQ with out a single glitch. It is a free download from RED.
OH... and this is the cool part.... RedRushes is 8 core aware. All 8 cores trans-code your footage so it is pretty snappy compared to FCP. The 7 hrs of footage I just trans-coded took my 8 core Mac Pro exactly 12 hours! Not bad.