NOTE: For this post, please keep in mind that the audio is always in sync with video!!
This is a little annoying. I was happily editing away when suddenly I noticed a significant shift in the waveform location between my track one and track two. For example if the two pop occured at a certain location for track one, the waveform for track two would indicate that it was at least one second before. Then suddenly both tracks became drastically out of sync with the video. This is only the waveform, not the actual audio.
So as I am relying quite heavily on the waveform for editing, this has really screwed me up and is slowing me down a lot.
I've quite the program and rebooted but the audio is still out of sync. It's quite bothersome (adding to a list of bothersome things, like magically muted tracks and such).
Try deleting the Media Cache with PP closed and then reopen the project. Let it rebuild those cache files.