I've had this happen to me a lot; it's a huge pain! It could be a number of things, but it is generally caused by long renders, and the audio/video of the source files don't match up (digital footage isn't perfect).
What I do is render the timeline clip by clip until I find the clip that can't render. Open that source clip in Cinema Tools and conform it to whatever frame rate you're working in (23.98 or 29.97) then reimport, and try again.