PP CC 2014 plays video fine from .mts files, but the audio is glitchy and jumpy.

Premiere Pro CC 2014
OSX 10.9.5
I have imported .MTS files from one Canon C100 into PP through the Media Browser. I kept the file structure intact from the camera when copying. When I play a file in the source or program monitor the video plays back perfectly; however, the audio is glitchy and jumpy. It will skip time, jumping forward and backward seemingly randomly. If I open the same clip in Quicktime 10, it plays back 100% normal. I have restarted, reimported, and even transcoded the files to Pro Res 422 using Media Encoder CC 14. Nothing fixed it. The audio glitches the same way in the transcoded Pro Res Files.
This is only the first of three cards of media. In total I have 120 .mts files in three separate AVCHD folders from a three camera C100 shoot. This leads to another issue I know I will run into. There will be three .mts files named "001," three named "002," etc. I have solved this issue in the past simply by transcoding, but that again failed to work for me thus far. So if I must stick with the .mts files, does anyone know a workflow for using multiple .mts files with the same name in one project/timeline?
Thanks

I find it hard to believe that this fixes the root of the problem as the same files playback fine in CS6. CS6 and CC 2014 should be referencing the same codec library on my system, right? If this is the case, then there is something wrong with how CC14 is decompressing the footage with the codecs that are working fine in CS6.
To further this point. I imported the same files into CS6. CS6 played them back fine, so I saved the session and opened it up in CC14. CC14 converted the project file and all media loaded and plays back normal now.
So if this is a codec issue, it would not have been solved by opening the files first in CS6. It also would not be solved as so many others report by moving the files and relinking to the new folder. It seems to me to be an import issue that is solely in CC14, not CC or CS6.

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