Yeah, I noticed that too. I converted the music over to mp3, and even though the music tracks are amplified as much as they possibly could be in Audacity, they're still quieter than their midi counterparts would have been. Yet another 2k3 "quirk." :(
I probably will lower the volume of the sound effects at some point, but it would take at least a weekend to go through them all!
Edit: Trying to find a DynRPG solution.