Why do some of my clips turn black after they are transcoded?

I've been using the same camera (Canon T4i) with the same computer (Macbook Pro) for over the last two years. I've never had this issue. Tonight, almost all of my files imported without any issues. I chose to "optimize" the clips and kept them in their original location They all showed up in my clip bin, but after transcoding, about 5 of the 36 files/clips I imported turned black with no audio or video. I can look in the transcoded folder and see that they're there, but they do not have a thumbnail and will not play in preview. I tried to duplicate one of the original files with a different name and it still has the problem after transcoding. All of my original files play fine. They don't seem corrupted. Anyone run into this issue?

I have the t4i and a 2013 iMac and developed similar problems when I added an SSD in a OWC enclosure via USB3. I was getting over 300 MB/s transfer rates and thought that this was going to be a great help until I experienced all the drop outs in the video I was importing. I found out that USB 3 has a "burst mode" and I think that was the culprit when writing the video. For complete disclosure, I was using a USB3 Hub to connect the drive to the system (not directly connected.) Since I save my video files onto a separate (firewire 800) drive when I copy them from the camera, I don't know if this is a system wide problem, or just with FCPX. My problem seems to gone away when I connected the USB 3 SSD device to an Akitio Thunderbolt "Dock" which I think throttles the USB3 stream somewhat (not a lot, but SpeedDisk showed slightly slower speeds afterwards) or at least communicates better with FCPX.
Anyway, you didn't state what your media pathway was, and I'm just basically asking: is a USB3 drive involved?

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