I found something interesting inside a .bin file tonight.
<NoMiniMap/>
Telling the client that the object does not show up on the minimap.
Now my guess is this......you could look in the .bin file for the items you want to show up in the Quest lootbag notifier and see if it has <NoMiniMap/> in the code for that loot bag and if it does then remove it and it might show up on the mini map?