If you're rendering with GC on in Firefly make sure you set your transparency maps (and basically any greyscale maps) to GC 1. If not, they will not render correctly. You can easily do this for everything using greyscale maps in a scene by going to you menu Scripts:MaterialMods:changeGamma Enter a value of 1, OK, select all props and figures, OK, select all of the above, OK and you're set!