I am not sure but I would be suspect of a hardware problem, possibly the hard drive. It might be writing the registry incorrectly and corrupting it enough that windows detects it and tries to repair it. I have only had that happen a couple of times where it did it continuously and I have worked on a huge bunch of machines. It seems like maybe once it might have been due to bad memory as well. It could even be a faulty motherboard component. The registry, to the best of my knowledge, is constantly being manipulated while windows is running and it sounds like during that writing to the registry the corruption is significant enough that windows recognizes it, probably finds some type of read error when attempting to read it. Of course I can't be sure but I would suspect hardware problems.