First off, its new years so you should be out getting hammered.
ATV2 preset works fine with Ac3. Not sure your issue but the preset itself is irrelevant. If your file your encoding is DD or DTHD, you can use passthru but if its DTS youll need to do AC3 (which encodes to DD).
What type of file are you converting? What does media info say about the file type?
PS when in dounbt, make sure you are using a nightly build of handbrake and not 0.9.4