The other icons are fine because they are icons created for KDE apps (amarok, and kopete for instance) however aMule uses a tray icon created with wxGTK. The problem is that KDE doesn't sem to properly recognize the way GTK uses transparency, therefore the icon looks good in GNOME, but sucks in KDE. I have no idea if this can be changed, however (I hope so, I also love KDE 4.2.1)
Regards.