Well the weird thing is that if I make some changes to the model, save it then update the model in layout sometimes it renders it properly without me ever touching the style settings or the material itself. Which happened to be the case for this model I was working on which magically worked after some revisions to the model. I don't get it, it seems to be a bug.
Charlie, I noticed that in the left side of the images you posted the transparency of the two pieces of wood are different in the images and I believe worked properly in the first image (Faster) but not in the second (medium). Also I just noticed, at what appears to be a bottom rail of a railing, when it hits that column it is rendered really transparent in the third image which does not seem proper to me (and is a lot more than the first image). I could be wrong though. There is definitely something wrong with looking through 2 transparent materials.
jsteacy