How can I conform clips without a problem?

Conforming over 2000 clips in both Premiere Pro and Prelude result in skipping audio within the clips. I've tried cleaning media cache, but the files re-conform with similar problems (although in different places). Any suggestions on a reliable way of knowing that clips will conform correctly? I am using Canon C100 footage. The glitch can be seen in the waveform below:
Any tips would be much appreciated
Thanks!
Josh

Just an update on this. I have since been able to fix the problem. I had changed my Media Cache folder to be on an external drive. Each time, I would clean the media cache and delete the relevant files from the Media Cache.
It turns out, that when I first started editing with Premiere, some of the media files were cached at the original directory on the local drive. I have since gone in and deleted all of those files. With a reimport/conform, all seems to be fixed!
That took a while.
Thanks again for your help!
Josh

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