Regarding my ffmpeg settings, I'm using the standard version that comes with kmttg. I've not noticed any issues with A/V drift.
FFmpeg version SVN-r21085, Copyright (c) 2000-2010 Fabrice Bellard, et al. built on Jan 8 2010 06:05:02 with gcc 4.2.4
configuration: --enable-memalign-hack --prefix=/mingw --cross-prefix=i686-mingw32- --cc=ccache-i686-mingw32-gcc --target-os=mingw32 --arch=i686 --cpu=i686 --enable-avisynth --enable-gpl --enable-version3 --enable-zlib --enable-bzlib --enable-libgsm --enable-libfaad --enable-pthreads --enable-libvorbis --enable-libtheora --enable-libspeex --enable-libmp3lame --enable-libopenjpeg --enable-libxvid
--enable-libschroedinger --enable-libx264 --enable-libopencore_amrwb --enable-libopencore_amrnb
libavutil 50. 7. 0 / 50. 7. 0
libavcodec 52.45. 0 / 52.45. 0
libavformat 52.46. 0 / 52.46. 0
libavdevice 52. 2. 0 / 52. 2. 0
libswscale 0. 8. 0 / 0. 8. 0
I did upgrade Handbrake from 0.9.4 to 0.95:
C:\Users\Home\Tivo\handbrake>HandBrakeCLI.exe -u
[11:22:20] hb_init: checking for updates
[11:22:20] Using http://handbrake.fr/appcast.xml
[11:22:20] latest: 0.9.5, build 2011010300
[11:22:21] hb_init: checking cpu count
[11:22:21] hb_init: starting libhb thread
HandBrake 0.9.5 (2011010300) - MinGW i386 - http://handbrake.fr
Your version of HandBrake is up to date.