Angelo thanks for the response. I think I’ve narrowed it down to whats causing my issue.
To explain more the issue, its not the .pek files that are causing the issue, its the .cfa files where Premiere appears to retranscode the audio files.
I use several tools to transcode all my files to Pro Res 720. The only time I have the cfa file creation is when a file was transcoded in Episode (by Telestream). I believe this is causing my issue.