I managed to work out the one with Gold and platinum (i.e I actually now understand the output zones, the input zones and the general rules the game works by). Since then I have done another level or two and it's starting to click. This is largely because I understand the programming tools I've got to work with and the way the game works and it's interface.
I still maintain that the tutorial is poor. Sometimes it is adequate but other times it's not. I was patient and stuck with it because I saw the potential in this game (I suspect that many others would dismiss it instantly). It's not a lot of fun trying to solve a puzzle when you don't know the rules to play by.
I've got background in Chemistry (not that it matters much here) and understand mathematical programming and algorithms but I imagine it must be massively difficult to understand if you are staring from no experience in it at all.
If you look at the flash games the same developer made you'll notice the same thing. The learning curve is practically vertical, but once you understand it you feel like a genius every time you get through a level.