I have heard on the MCF (shudder, I should make you pay me for going over there to do research ) that sometimes when you use World Edit to move stuff around it can corrupt the data, making blocks vanish, that could be a cause.
One thing to add is that all of the blocks vanishing were placed by players not generated.
As for the chunks, it wasn't as drastic as the ones in the link you posted, it is mainly 3 or four blocks (from what I have seen) that just disapear