I don't have MediaFork so can't report any bugs on it.
I am however currently trying to convert from DVD (both PAL and NTSC) into H264 / AAC for my ip00d with some, not terrific, success. Handbrake seems to be about the best of a bad bunch for this particular job - Videora mangles the start video frames, VLC mangles the output frame rates.
I'm using the CLI with HBTest under Windows 2000, HandBrake 0.7.0 (2005110400).
Do you guys want me to post my HBTest audio bug or is there somewhere I can get a test version of MediaFork to see if yours works?