3) Make sure that the Root Folder is pointing to the correct path.
I had an issue where our server defaulted back to C:\Documents and Settings\All Users\Application Data\QlikTech\Documents. This caused my Named User CALs to get messed up, because the PGO files were located in a different directory.
Once you set the correct path, the QEMC will restart the QlikView Server service on the server and you should be back in business.
The most likely reason when this message appears is that you are running two servers in the same network with the same license, and that this license does not allow clustering. Think for example in a hardware update, where you have the old computer and the new one both with QlikView Server services running.
Usually the issue is fixed when you stop the QlikView Services in the Windows Services Console in the old computer. As soon as QlikView sees that is running the only license valid, it goes back to normal.