Audio too fast on locally streaming content.

I have an Apple TV 2 hard wired to my Airport Extreme and I'm streaming videos from iTunes on my Macbook and on some videos the audio is too fast. The characters sound high pitched and it goes off sync with the video. When I made the videos I ran them all through the same preset on handbrake. When watching them on my MacBook everything is prefect. But when I use the Apple TV to watch them using Home Sharing (not AirPlay) the audio speeds up. The funny thing is I re-downloaded one of the videos and re-encoded it and that same video gave me issues again. So far I'm only seeing the issues with two of the videos, but I'm not sure why it's only an issue when streamed. I tried AirPlay though iTunes and the same problem. However if I open it with Quicktime and mirror the display I don't have the problem.

Thoughts fixes?