Emulator

The game has built in reverb effects that weren't emulated in HLE before the New-AX-HLE Merger. They are pretty much everywhere in some capacity. One of those effects is a constant reverb whenever in the dark realm. I can tell you were in the dark realm for that cause of the music. So I didn't believe you at first. You should have recorded in the light realm with music off, in an openish area without reverb in LLE.

So I tested it myself, and there is definitely something screwy going on. It sounds like the reverb effect is applying where it shouldn't and is cranked up to 11. Here's a comparison of LLE and HLE audio for the power beam at the start location near the ship. It affects all sound effects, but you ALWAYS have the power beam, so this is very very easy to reproduce. Just turn off music, go to the quiet spot at the beginning of the game, and fire away. I kept it as a video to make it easier to reproduce. Video is small cause dialup, and audio is more important here.

DSP LLE - https://dl.dropboxusercontent.com/u/519564/MP2LLE.mkv

DSP HLE - https://dl.dropboxusercontent.com/u/519564/MP2HLE.mkv

Also, the in-game "Surround" setting appears to have no effect, unlike what the op said. Of course, I don't have a surround speaker system, so that's possibly why.

DSP HLE with Surround (recorded in stereo by fraps) - https://dl.dropboxusercontent.com/u/519564/MP2HLESurround.mkv

Metroid Prime 2 Tri also has this problem (remember to turn on DSP on Thread or you will regret it). Prime 1 GC, Prime 1 Tri, Prime 3 Wii, and Prime 3 Tri are all unaffected.

Reproduced in 3.5-1210 win64.

This issue is fixed.

Don't know if this is the exact build.

http://code.google.com/p/dolphin-emu/source/detail?r=9b128e9347ce5f7a46c313f5f76b3a32dfbe9001

I'll mark this issue as fixed if burnhellpsp or MaJoRoesch confirms it's fixed.

BTW, "Surround" has sound effect issue yet.