I think the problem isn't that sides are missing or disapearing. It looks like the problem is that you can see through the top color to the color behind it. This is making it appear as though sides are missing. Any ideas on how to make it not do this?
I was experimenting with drawing triangles and the bottom one would sometimes draw on top of the top one. I went back to the cube and only displayed a couple sides and could see that is what is happening there too.