I am having the EXACT Same Problem with some Star Trek DVDs
I ripped them with DVD Decrypter 3 in File Mode, all the IFOs, VObs, etc are there in the Folder.
Fired up DVD2One and it simply quits sometime during the transcoding, no "FINISHED SCREEN" is presented saying that it is done. When I look into the Targetfolder the VOBS are there - but IFOs etc.
BTW; I am running WinXP Pro.