Video is indeed out of sync in that example. And again CloneBD and Mobile will fix those. SlySoft used mencoder as transcoder and now switched to ffmpeg. But both applications are somehow buggy concerning timestamp handling so SlySoft again will switch the transcoder.
We will now use our own transcoder that uses libavcodec and libavformat (from FFmpeg) to produce correct and accurate movie files. This takes some time to develop as you can imagine. The new transcoder engine is capable of reading and creating DVD, HD-DVD and BD streams and has an extremely accurate timestamp handler.
The new engine will be able to decode all audio streams (except DTS HD in lossless mode), all subtitles (HD-DVD and BD) and can downmix DTS and EAC3. And has of course all the features that CloneDVD, CloneDVD mobile had. Plus many you requested like multiple subs, better automatic black-border handling, audio preview, matroska format with chapter information to name a few.
This new engine will first be integrated into CloneDVD mobile. So look out for something with version 2 in a few (months|years).