Hmm, that isn't the issue that I'm having, saving maps as 0,0,0 always works for WA transparency.
The issue is that I cannot "Paste As Transparent Section" over anything, usually the background would be transparent, so I can place objects over other objects without the background colour being there.
With this issue that only started happening today I cannot do this anymore...
Though, that is a good idea because I can load whatever image I have, into WA as a black image, it will save it as transparent, then I might be able to load it back in as a transparent image... I'll try it! Though I'm not sure that will work the way I hope it will.