I am not sure if it’s a CS6 bug or not but I do occasionally have the same type of problem or worse, I get artifacts and noise appearing on the exported video.
It doesn’t happen all the time but I notice that if my assets are on a USB 3.0 drive and that I render on the same drive, I do sometime end up with issues.
Solution: export to a different internal drive. It’s the only work around I found so far and 100% of the time it solve the issue.
All my assets are AVCHD / MPEG2 and they are always exported to uncompress .avi out of after FX.
I have a Nvidia 570 with latest drivers in my system and all SSD drive inside and USB 3.0 external drives.