I can't think of anything... If its not the HDD, then it must be the logic board? Or a component on it, such as RAM, CPU or less likely, the GPU?
Try replacing all the ram with just one good ram stick for starters.. I'm just spitballing some ideas here.
A way to circumvent the problem would be to download the updates [http://support.apple.com/downloads/#macosandsoftware|directly from their site] instead of using software update.