Perhaps I should back up and explain that the intention of running the clips through Log and Transfer is to transcode them to Pro Res 422 without losing the timecode. Most of the time I will run these clips through Streamclip which does not preserve the timecode, however I needed the timecode for a sync job this time.
I have the Canon plug-in installed and the files do indeed import through log and transfer. I was just trying to figure out why only some of them transcoded properly and if anybody has encountered this problem before.