Using the now working audacious-gtk3 as a reference:
The .desktop file includes two references to icons
Icon=audacious-gtk2
X-FullPathIcon=/apps/audacious-gtk3/share/pixmaps/audacious-gtk3.png
As audacious-gtk2 is not located using the find command, presumably it is audacious-gtk3 that is being used .
xmms.desktop includes two references to icons
Icon=xmms
X-FullPathIcon=/usr/local/share/pixmaps/xmms.png
Perhaps this should point to /apps/xmms/share/pixmaps/xmms.png