Yes, I've read the Shaders page.

Now, on previous versions of Toribash I've had shaders work fine (even though I am running a fairly old rig, with a RADEON x600). Yet on 3.9, I've been unable to do shaders because it turns both players invisible. Can anyone help?

I guess there were some modifications made in the 3.9's shader engine so it requires slightly more stuff then it required before.

What I can advice is that you update your graphics card's drivers.