Currently I am converting them ready for my iPod Touch which i should be getting shortly. I am going to try and rip another DVD in iPhone Preset to see if that helps. The audio problem exists when playing back on a laptop. which always gives a good performance so I highly doubt it's that to be honest.
EDIT: i just tried a couple of chapters of an episode of Hustle. It's still there, it's so very close it's just hard to ignore once it's there.
Any suggestions apart from "Live with IT?"