Which is why I use Nero first, before the imToo converter.
DVD's are made up from a bunch fo VTS and VOB files (aswell as BUP's). YOu need a programme to read the video as a whole, then encode this to one single mpeg file. Nero Recode does this, and recodes the DVD to an MP4 file.
I use imTOO to then transcode from MP4 to WMV, or MPEG 1/2, etc for whatever reason I might need to.