Note... The technical reason for this is:
AC3Filter handles AC3 and DTS audio decoding. The DVD you are using HAS AC3 and/or DTS audio (probably AC3) for surround-sound support. However, like many DVDs, they didn't encode all of the audio to AC3 on the disc, but only encoded the "main movie" file to AC3. All of the menu and extras audio is probably all just 2-channel PCM audio (essentially WAV audio).
The problem is that AC3filter can't decode PCM audio. It is getting loaded when you start the DVD because the DVD supports AC3, but only for some of the media. AC3filter doesn't know what to do with the PCM audio and just ignores it.
It's actually pretty stupid that AC3filter doesn't either handle this itself, or pass it back off to DirectShow for a different filter to handle it. Perhaps it works correctly with newer versions, but this is the same behavior I've seen before when using it. (Actually, I just looked and they claim that MPEG joint audio is fixed in the newest stable build -- who knows.) Unless you are using AC3filter for some really fancy stuff, I'd just get rid of it and use FFDSHOW instead. It is just as capable in almost every way, and far less troublesome.