FCP Log and Transfer not converting entire files

Shot on Canon 7d's. I'm having a weird problem with FCP. When I use Log and Transfer to convert files it often truncates these files. I checked to make sure I didn't accidentally put a marker for in and out into the original in the L&T window but I did not.

So, for example, a 9 minute video file gets transferred but is missing the last 2:30 of video.

Any ideas on what might be causing this? I have plenty of space on the capture drive, so it can't be that.

I am going to Apple ProRes 422.

Thanks in advance for any help you can offer.