I personally like the first of the three the most. It does look better without the filled-in sides (original logo) to me.
I like the New Logo Black/White best as well. This one is feels simpler and not as 'heavy' as the fully filled in version.
I played with your image a bit, and did this, sort of borrowing on what Kip had said, and I think I stumbled upon the thing that keeps bothering me (it's probably just me)...
Anyway, I think it's the isometric view that is bothering me for some reason. I realize that it's not as easy to show the actually-a-true-cube nature of the project with a perspective view, but isometric just looks off to me. The other thing that wasn't apparent to me until I took away the outlines is that the letters are pointing 'down' (as a result of the isometric view). With the lighter-weight outline, from a distance (or in a thumbnail image) it might look better for the letters to aim 'up'. That, unfortunately, also introduces its own problem in that the isometric view is now showing the 'bottom' of the cube.
Anyway, just my random thoughts.