Well, I worked out what my transparency problem was - apparently it doesn't like using an image that already has a transparent colour for a masked texture. Once I exported the texture map again as a normal .png it worked fine.
Unfortunately I'm still not having much luck with the vertex colouring. I used the EntityFX thing, and it made my model disappear altogether!
Unfortunately I'm still not having much luck with the vertex colouring. I used the EntityFX thing, and it made my model disappear altogether!