Yes I have the same issue too. Disc 1 and 3 rips just fine but disc 2 and 4 won't work.
I don't know why but that's what I am dealing with. Don't know if there is a solution or not but I gave up. Now season 10 in my tv shows is missing 2 dvd's worth of shows.
Did you use hand brake for your tv shows?
Also if you did please let me know your exact settings for this. I used another program called Cucusoft and stuck with high rez ipod setting in MPEG-4 format not H.264.
I'm just wondering if I need to use H.264 and re rip them all or leave it as is?