I've decided to rip a pile of my dvd's that have been neglected (dvd storage makes everything difficult to get to). I'm using Handbrake to create deinterlaced 2500kbps H.264 MP4's (*phew*), however from time to time, the final MP4's suffer a complete audio dropout after about 2/3 of the movie through until the end. The dropout seems to vary from attempt to attempt, and it doesn't seem to matter if I use the actual dvd, or if I use MacTheRipper to rip the dvd to the hdd, then use Handbrake on the image.

The only symptom I've noticed during the rip is that the fps drops significantly around the same mark that the audio cuts out. While it may start at 19-25fps, it dips to 5-8fps, and stays there for the remainder of the rip.

I have a bunch of MP4's that are fine, but it's irritating to leave things running while I'm at work, only to come home and find a virtual coaster as a result. Right now I'm assuming that the computer is choking during the process, but if anyone has a really obvious - or not so obvious - suggestion, I'd appreciate it!

Yep, I've experienced the same problem - seems to be a known "bug" somewhere. A post on the handbrake forum discusses it in detail

As the discussion states doing a full disc extraction with MTR appears to help.

Bugger, that's quite a thread...

I'd still like to get my library onto disk, if anyone has any suggestions of alternative apps?

I've been using fmpegx - not into apple tv format though.