Software: Sony Movie Studio Platinum 12
I'm running into a seemingly random problem creating dual point of view videos. At some point in the rendering process the second video track will randomly "become" the first track. The videos were created using two Hauppague HD PVR2 outputting the video to .mp4 containers.
Example

(the problem starts @ the 7 minute mark)
Track 1 - Video A
Track 2 - Video B
Left Side Video A | Right Side Video B (all things normal)
Left Side Video A | Right Side Video A (randomly changes B ->A)
I've checked the video files, and they play fine using VLC. Could there be something wrong with the video file that causes Movie Studio do this and still be able to play fine in a media player?
Any ideas or reccomendations (or am I leaving out important troubleshooting information for you to help?)?