I've not had issues with that application cause I use Sony Vegas and Adobe Premiere for the editing. However I have had similar issues before and what I've found is the original file being used is partially corrupt, so I've hard to start entirely from scratch.
The problem of course with doing this is the time involved.
I'm not some computer guy so you can explain to me. Can a file be corrupt from a DVD which has simply been recorded or transferred from a VHS?
Shall I change the application I use to convert the file? I think off the dvd's they're normally VOB files. I use any video converter and haven't had any problems really. What is the best converter to use to maintain quality and what file format is best?