that certainly is a strange problem. The only thing i can think of is following the steps in that link you posted at the beginning. Along with that, it could still be caused by the updates? is this something you have checked? as if your server pushes out apple updates it could be trying to download a huge amount of data for the updates (this may not be the case but its worth a try) If you have had your server for less than a year you can phone apple themselves for some support which you get with it when you buy it. If not you could try phoning them anyway their normally quite helpfull and if its an issue they've seen before they will most probably be happy to help you.
Hope this is of some help, let me know how you get on
Jo