Hi,
I had a similar problem. I cannot explain why it happens but I can tell you a way round it if you have suitable software.
I would import the entire video/audio file (AVI in my case) into an audio editing program, I used Adobe Audition. From this I would export the videos audio track as a seperate MP3 file.
I would then go back into Premiere Pro 6.5 (As I had at the time) and import the original AVI file. I would then lock the video track and delete the original audio track replacing it with the new created MP3 track I had just created and then the problem was solved.
Its a pain in the backside doing it this way but it does solve the problem if you find no other method.
Mark
www.onlinevideosolutions.co.uk enquiries@onlinevideosolutions.co.uk