Ok, so the reason why the upgrade from the Instance Manager is failing may have something to do with the upgrade also failing from the Management Console.
In the OP you said that the upgrade fails even from the server GUI (I assume you meant he Management Console).
Could you tell us what error you are getting when you try to upgrade when you log into your Management Console --> Settings --> Updates, and perform the update? Are you getting an error message in an email?
[EDIT]
Before attempting to perform the Update again, please go to Settings --> License, here press the "Edit" button, then OK. If it throws any error about missing information, please fill in all fields first, then press OK again.