It depends what you’re sending it to, over HDMI.
If you’re sending 5.1 over HDMI to a receiver that can decode 5.1, then you’ve usually balanced the system when you first set it up, and it should be sounding like any other AC-3 signal, as far as I know.
If you’re sending 2.0 stereo over HDMI to your TV (since most TV’s won’t decode AC-3 at their HDMI inputs), then this simply sounds like the same issue everyone perpetually has with the audio when AC-3 5.1 is downmixed to stereo – the sound effects and background music are too loud, and the center dialogue channel is too quiet.
This doesn’t appear to be limited to the WDTV itself.
When I play an AC-3 5.1 DVD in any of my stand-alone DVD players, the stereo audio out is the same – I usually watch TV with the volume at “10” or “12” and usually need to watch DVDs at “18” or “20” to hear what’s being said (and find effects like gunshots to be excessively loud – I took to watching DVDs with the captions on, because if it was quiet enough so that the effects didn’t disturb my sleeping family, I couldn’t hear the dialogue).
But, as far as I can determine, I note no real difference between the AC-3 track on the DVD itself, played through a stand-alone DVD player, the AC-3 track in an .iso file, played with my WDTV and the AC-3 track in a .mkv file played by my WDTV… the WDTV doesn’t seem to be doing anything “wrong” or different… it just seems like this is how consumer-level devices downmix Dolby Digital 5.1 to stereo. Whenever possible, I include the 2.0 track from the disc when I make my rips so I can avoid this very “problem”.