Issue with wave files from Pro Tools

First off this is mostly a problem with Pro Tools, but I didn't notice a Pro Tools forum, but I am working in Premiere CS6. Ok, so I am editing a feature documentary. My sound mixer did a final sound mix in Pro Tools. He used keyframes to mix all the dialogue and music, but when he exports to a wave file it seems like all the mix keyframes are gone and half of the dialogue is randomly peaking and not mixed with the music properly. He is using Pro Tools 9. Here is where the plot thickens. I had him go back and re-export one of the interviews that was severely peaking and upon exporting it again it was fine, yet when we re-export the entire 90 minutes the audio mix is haywire. Has anyone out there ever seen a problem like this before and know how to solve it?