I've been using my FS100 and FMU128 for about 90 camera hours and all has been good. When I would go to upload my footage from a job on Saturday via Log and Transfer in FCP 7 I am only able to download the first half. The transfer window shows the other half but it does not give a duration or a preview thumbnail.
How long is the clip? I'm not sure the exact limit but sometimes that will happen to me if the clip is over an hour. But you say it DOES L&T the first half? It does not give you an error message? That sounds to meier like you've perhaps accidentally set an out point.
After seeing that it was a frame rate issue, I checked it out in the FCP forum and found that FCP 7 doesn't work with footage that is 1080p @ 59.94 because it isn't a broadcast format. So yeah. I was suggested a program for this called Clipwrap 2.