I noticed that when I try and rewind on a DVD-9 created with Nero that it gets stuck at chapter breaks, you can't get back to a previous scene without actually skipping back to the previous chapter and fast forwarding. It doesn't actually start skipping chapters like you said, but problems all the same.

I've found the best way to burn DVD-9 is to rip an ISO using dvd_decrypter and then burn that ISO using dvd_decrypter. Or, if the movie itself is only 5-6GB, I'll just shrink it down and burn a dvd-5. Haven't had any problems with DVD-9s since. Now if only the prices on the media would drop....