Problem Upgrading Into CRM 2016

Hello Experts,

While upgrading my CRM 2015 (Update 0.2) into CRM 2016, The set up is stuck in System Checks window as bellow:

This happens when choosing to update the customized Organization (i.e. contains Autonumber plugin, some custom entities, SiteMap changes...etc).

However, when choose to upgrade an organization that does not have any customizations, upgrade goes ok.

Any help about this?