I haven't really noticed a sound quality problem on my DS and Moonshell. I usually connect it to the stereo in the car and it sounds just like my mp3 player. I did have some "clicks and pops" as well as music playing too fast in DS Organize, but that may be due to my SC Slot2.
If you want to try something different to check quality in Moonshell, try converting some songs to ogg format and see if there is a quality difference. As another user said, if Moonshell says "ID3 tags missing" or something similar, convert ID3 to V1.0, or try ogg.