A few users have reported issues with the latest version of Handbrake.

There is an issue with the latest version of Handbrake that does not allow us to transcode these files.
If you create a file with AAC (faac) encoding it be broken. We recommend you use ac3 encoding (pass-though or ac3 ffmpeg) for you sound.

There is also an issue with frame rates you should set the frame rate to 29.97. This is because if the source has variable frame rates Handbrake cannot process it correctly.