Hi John,
I hope you sorted out these sync problems. I don’t know if this will work in your case but today I had a similar problem where I transferred an Adobe Premiere CS5 project along with the video files to CS6. When I started working on the CS6 project, I noticed that the videos were out of sync although the clip timestamps were the same in CS5 and CS6. After trying everything I could to find out what the problem was, I deleted the .xmp files that sit alongside the original video files. This forced a reindex of the video files when I next started the CS6 project and all the clips were then syncronised !!
I hope this helps you and others.
Rob