Do you use dvddecrypter to demultiplex the vobs (stream processing)?
I tried demultiplexing directly from dvd with dvddecrypter but I sometimes got header errors or something with the ac3 files (I can't remeber exactly, it was a long time ago). So now I always rip the vobs to my hdd and demultiplex them using vobedit. Works like a charm, never had an error.