When running the Upgrade Advisor for SQL Server 2012 the textbox that accepts the server name will not accept port numbers and will give an error on the bottom of the screen that says:
"The specified server name contains invalid characters."
This creates a point of contention as we have instances of SQL Server that run on non-standard port numbers and DO NOT have the browser service enabled per our security requirements. Thus the port number lookup fails and will error.
Currently, the only work around is to create an alias with the correct port number - however I find this disturbing as the functionality should already exist given it's a normal part of connection strings.