Just an update on my last post. Springfeel hasn't given me a timestamp for the distortion yet, but I've had a listen to the scene in question and think I found what he's referring to. At 12:16 in the file there's what sounds like clipping. I've just listened to the audio coming out of my laserdisc player, going into an analogue amp, over good quality headphones and heard the same clipping. So it's either baked into the disc's audio or a problem with my player.
Given that I've been able to pass Bronan's DTS CD bit perfect test I'm leaning towards it being on the disc, but if anyone has any other way I can verify I'd really appreciate it. I'm still new to bit-perfect laserdisc PCM ripping so I want to make sure I'm not making any stupid mistakes.