Make sure you rebuild it on a closed, secure network. I had a similar thing happen with my RaQ4. Turns out I had been hacked within the 10 minutes it took me to get back to the box after the rebuild.
A little to my surprise that may have been it. I have no direct evidence of actual hacking, but a reinstall with the outside network connection unplugged did work. Thanks! Now I have my fingers crossed that I can get all my patches installed.