For those interested in the future, I managed to solve this issue by going through all of the folders created by the camera and pulling out all of the individual .mp4’s.
Essentially this strips the .mp4’s of all the extra additional meta-data. I then imported all of these mp4’s into Premiere and once conformed all was well.
Note: This method will require that you manually relink all of the clips that the ex-1/ex-3 has split up. This is because there is no longer any meta-data that tells Premiere that they belong together. Not a big problem but worth mentioning.
Thanks for the help 🙂
Cheers,
Brad