When you copied the audio into /system/media, did you do it manually or do they (Team Liberty) provide a script to do it for you? If you browse to /system/media with Root Explorer or Super Manager, is the audio file still named drwho.ogg or was it renamed to something like android_audio.mp3 or ogg? I know of two ways to enable sound.
The first method I found was here. With this scripting, the audio must be renamed 'android_audio.mp3'. Obviously the desc.txt within the bootanimation.zip must be modified to point to this file. I'm certain an app or script could make these changes automagic so the user doesn't see what's going on; it just works. That method could be modified to fit a rom, so it doesn't have to be exact. I wonder if Team Liberty implemented something like this?
More recently, another option became available. This second method is the one I recommend, unless you are using a Gingerbread rom. Replacing the /system/bin/bootanimation binary with the one from the D2 R2D2 edition enables sound. An additional benefit is that animations tend to play very well in sync with audio, even on my D1. Apparently, even 24fps animations with sound play in sync better on my phone than your DX. Unfortunately, this binary was released on the D2R2D2 running froyo and works well on froyo roms, but the GB roms out there all seem to break it. I've been told there are missing symbol(s) in the EGL library. Once GB hits the D2R2D2, I'm hoping an updated binary or other fix will become available.
I'd suggest attempting the 2nd option. It can't hurt to try it. I've been told boot animations won't play if running the updated binary on a GB rom, but I don't suspect it would be affected by the 1st option scripting. Just rename your current /system/bin/bootanimation something like bootanimation_nosnd. Don't delete it, as if you do upgrade to a GB rom (or some other reason), you'll need to revert back. Copy the updated D2R2D2 binary in its place, duplicate the permissions, and give it a reboot to see the difference! Don't forget, you'll probably need to delete the android_audio.mp3, so you don't have two instances of it attempting to play at the same time. I'd recommend using the original naming in my animations. I keep all of my sounds at /system/media so I just plop in whatever bootanimation.zip I want ATM.