Yeah, the alpha thing is annoying, as far as I can tell it's 3D Box weirdness.
I've found that engine I posted is actually pretty crap, once you add a few hundred boxes the framerate takes a big hit. I've improved things by taking the redundant stuff out of the loop and removing the family attribute--adding the repeated code back (like I did for the competition) in for the most common static features like walls and floors.
Special bonus screens:
Also: LD14 results are in. Standard Waiver got 7th Overall and 5th in the Technical category out of 121 entries.