strange problem - i downloaded the latest 5dmkIII SW a week or two back when I still had the T3i only - had the same problem with eos utility options from "Control Camera" tab greyed out. Yesterday after my 5dmkIII was plugged in- same problem. I tried playing around - uninstalled the device from the device options menu and after I tried connecting the 5dmkIII again - presto everything started working. Could use eos utility as it is meant to be.
See if this helps.