The reason why I kept asking you to run the 64 bit version of the utility was that I assumed that all of this related to ArcGIS Server. I, incorrectly, made that assumption based on the fact that you were discussing Windows Server 2008 R2 as the OS.
It is now clear that you have a server which hosts ArcMap using Citrix. In this case using the 32 bit version is the correct thing to do. Apologies for the confusion.
After so much discussion it will be good to see what the resolution of this issue is. Let's see what ESRI comes up with....