I just loaded the original tutorial's TGD files and they appear to work the same in TG 2.5, TG 3.3, and TG 4 alpha. So... I'm not sure what's wrong here. Martin, after our experiments recently, Matt reminded me that for a procedural (not a heightfield or image as in your original examples), the cloud will be evaluating the noise function *at the altitude it's shading at*, so it's evaluating the shader at a different point than the terrain and will look slightly different as a result. Something to keep in mind...
So I don't think anything is wrong at the moment. But if you can provide an example of something not working as explained or expected, do let us know!
- Oshyan