I'm just guessing here, but maybe the faces that are missing all have more than 4 sides. Blockland uses quads, so, I haven't really tested it out, but maybe anything with more than 4 sides gets thrown out.
(If you do test this make sure the face actually has more than 4 sides. If there are lines down the middle of it, chances are it's been split up a bit.)
EDIT 6/21/13: Just realized that can't be the problem, some of the side faces(which are quads) are also invisible.
V Try recalculating normals. V