.mov problems

I'm currently working on digitizing a collection of videos at work from Mini DV to .mp4's.  I'm using adobe to capture the video through a Thunderbolt to Firewire to DVLink. I have Scene Detect on and for the most part it is working smoothly. The issue is, on some random clips, they will not be imported with the video attached...  Only audio.  If I go to the containing folder that I am having the files stored in, I can watch the video and hear the audio like normal in VLC or Quicktime, but as soon as I bring it into Premiere its as if its only an audio file... All the other .mov files work as normal.

Here is what I have tried:

1. I have tried changing the file extension from .mov to .mp4. When I import it I have both audio and video but the audio is completely off, and the video is choppy.

2. I have cleared my cache (I read somewhere here on the forums that, that helps). I have renamed my cache, relocated my cache, I honestly dont think that has anything to do with it because I've fiddled with it a bunch.

3.  I have shut down the computer, I have terminated Premiere.

4. I have tried importing footage the "right way" by importing through the Media Browser

So far the only thing that has worked for me is taking the clip, opening it in VLC and exporting/converting it to .m4v.  I don't want to perform this extra step, so is there anyone here on the forums that knows why some .mov files work fine where others do not?