I like the colored dots for color repetition etc.
The boxes won't effect our decision, I like the ones in the current #1 slot better than newer version, but if you take the prize then they will need some minor tweaking regardless so you don't need to worry over it.
I would in general like to see a more rounded edges on the cubes and I am not sure of the current orientation of the cubes either but there is just something that feels a bit wrong about the current positioning.
Anyway here is what I mean by rounded edges
http://www.shutterstock.com/pic-11270614/stock-vector-black-cube.htmlAlso as to the motion, I would really like to see this in the orbital arc (think of the wake a boat leaves behind it) but again this is a minor detail that can be tweaked if we accept the design, overall it's very nice.