I had a similar problem with one of my discs (I don't remember which one).
What happened is that DVD Decrypter ripped the whole disc just fine, but when I tried to transcode it, I got an error about an encypted file... It turns out that for some reason, DVD Decrypter did not "see" the encryption on one of the VOBs.
The solution for me was to change DVD Decrypter to Brute Force first in file mode. It then ripped all files properly and the issue was gone. I don't know why this one VOB fooled DVD Decryter in CSS mode, but there it is...
I think that DVD Decrypter is by far the best ripper currently out there and consider myself lucky that I have never had to resort to using anything else!