I have embarked on a similar project. So far I have ripped 213 DVD's. But, there have been 8 that did, just what you are describing. I have a PM and MP both working on the project and tried the DVD's in both. No luck. I did not have a lot of time to mess with it. So, I just used MTR. I have lots of disk space, and do not mind some of these DVD's being large. In summary, I have experienced the same thing, but cannot offer a solution. Sorry.
I have tried to rip Talladega Nights as well ( a few times with different settings) and cant get it to work. I have ripped like 300 some DVDs into my library so far, and only TN, and Donnie Darko have given me problems. Annoying for sure.