The Partitions unaligned error message can often be seen after cloning but it will not affect the CUCM.
What browser are you using? Have you tried with IE/Chrome/Firefox?
I was using IE11 when I got the error in the Collaboration 9.1 Lab.
I originally assumed the partition error message was causing issues since I could not select anything from the CUCM toolbar menus. Therefore, nothing could be set in CUCM in the 9.1 Lab.
Since I got the same issue a couple of times setting up the 9.1 Lab, I decided to set up a 10.5 Lab instead. In the 10.5 Lab, I did not get the error and I was able to select options from the menus. I was also using IE11 with the Collaboration 10.5 Lab.
When I am using "Cisco Unified CM Administration" in the Sandbox, I am getting the following message;
ERROR-UNSUPPORTED: Partitions unaligned
I am also unable to select anything from the menus. Please provide me some guidance in getting the Cisco Unified CM Administration working.