I’m not quite sure why this happens in FCP 6 but I’ve had the same issue transferring long takes. I think it’s a software bug or something. Try grabbing them in segments around 10 minutes long and making the out point the new in point for the next clip. When you string them together they should play fine. That’s the work around for the time being. I’m sure someone else with a little more knowledge can explain why it’s doing this. If I recall, the earlier version of FCP did not have this issue.