Syncoper - what kind of computer are you using? Are you using a MacBook with the DVD Player program?
I've only just got around to watching my copy and I noticed this problem immediately, but like everyone says, switching the compression thingy off on the DVD Player program fixed it. It didn't occur to me because I've never had a problem with DVD sound before on my laptop, and normally I disable any kind of option like that which affects the actual sound, so I didn't even know such an option existed. The picture on mine was a bit jittery as well (not sure what's causing that) so I assumed there was some kind of problem with the whole film. I need to retract my vote...
As a rough guess, I might say that it affects the Opeth DVD and the one that Demigod mentioned because there's more of a fluctuation between levels with Opeth than there is on many DVD mixes for movies etc. Generally for TV and DVD everything is compressed quite flat, and the same for music also. With the compression on in this DVD, I found that when the heavy parts kicked it they had no impact because the compression made it quieter. That's actually something I've noticed on a lot of albums released in the past few years - there'll be a clean bit building up to a heavy bit, but when the heavy part kicks in it has much less power than it should because the whole thing is compressed to roughly the same level. The good thing about Opeth's mixes is that they still have some dynamic range - if you load the mp3 files into Pro Tools or something, you'll see that the quiet bits are actually quiet, whereas a lot of CDs these days just come out as a solid block. So, basically, I think it's a side effect of it actually being a good mix.