Audio sync while encoding in sections.

I'm encoding this video in sections because some parts are progressive and the other parts telecined. When i put the video back together it looks fine but when i put the audio back together it goes out of sync where i had ended/started a section. Anyone know where i went wrong? If you need the specific steps that I did i can explain.

Please do explain with more details what you've done.

Just take the audio of your original source and use that as the audio of your processed video. If the processing was done correctly, it should be in synch with the video.