I do not recall seeing a post about this, so I figured I would give a quick heads up to those who are using Log and Transfer via the Canon Plug-In where it may bite you.
To work in Final Cut, the video needs to be transferred to another codec and Canon came out with the plug-in awhile back which allows the cards to be read into Final Cut and logged. Very nice, keeps the timecode so you can easily know which clips were shot at what time, which is helpful when shooting multiple cameras in particular.
But there are a couple of gotchas. Broad stroke - the first is that the Plug-In may not import the entire clip, though it is reported as fully bought in. For example, a 5 minute clip may wind up being 1 minute when it is done processing, though the logging window has the actual running time. The second is that if you try to re-import the failed clips, the numbers change on the re-imported clip.
Not a big deal if there are not many clips and you can check them. But if you have alot to import, it can be a PITA. There are some suggestions on how to avoid the issue, such as by making sure that you mark in/out points or change certain preferences, but they did not work for me. Real bummer.