V6 will grab the VOB file for you from a homegrown DVD. Go to File > Import > DVD camcorder disc and follow the prompts. You can then add the file to the T/L, edit, and re-render away. There will be quality loss!
I'd bet it's a hardware problem, then -- perhaps the DVD drive. The original DVD drive I had on my computer (an older model NEC 4X,+R) had problems reading certain computer made DVDs; a new drive read the same problematic disks easily.