SlySoft has already examined the files and found nothing . . .
I doubt ripit4me "fixed" it. If you look around the net it seems there was a batch of BOBs that had a flaw on the bonus disc. Actually if you watch the original bonus disc you'll find that at one point it just stutters on most players, but will totally hang some. I think it's during a short film that the guy who played Nixon did. If you blink you miss it on the players that will play through it.
Anyway, I saw some posts where other rippers would rip it but they all had the same flaw in the backup, which I guess is to be expected -> garbage in, garbage out!
It seems that the discs exhibiting this flaw were mostly sold around Christmas of 2004. Try find a disc made before or after that period and you shouldn't have any problems at all (that's what I did and it was no problem at all to rip with AnyDVD. I compared the files and there's no difference between the flawed discs and the newer ones, so it's definitely a media flaw problem. For giggles I just tried ripping it again and AnyDVD v220.127.116.11 is having NO problems with the later replacement disc).
Now, off to find a ripit4me forum so I can go answer every post reporting a suspected problem or bug with "get rid of ripit4me and use AnyDVD" . . .