Could you elaborate on that? There's also a click sound played when you use a piece - maybe that's the source of the clicking?
Well, it is a quite frequent sound (more than once/sec), seems like it is the base sound that gets a bit messed up, but just guessing here. The melody itself seems OK. I was testing on a work IBM laptop, probably with a pretty crappy sound card. Haven't experienced it before though. Sound is way better on the vids on your site, but a different song.
We're using FSAA so it should automatically be anti-aliased. Maybe your video driver doesn't allow software to turn on FSAA? There's also an issue on Mac where we're not able to enable FSAA.
Well, the rest of the GFX (blocks gradients and more) looks just fine, but that could naturally be pre-rendered. Here is what it looks like. I think your screenies look better, but hard to tell, since they are scaled down.
Here is what it looks like:

As I say, it is a minor thing, but it sticks out, with everything else looking so good.