I ran into this issue on SQL 2016 when we installed a QA box and took the default NT service\MSSQLServer account to start the SQL server service. Then we tried to change the account to a domain account after the install. We could only connect through IP from remote desktops in SSMS.. Changing the account SQL ran under back to the NT account fixed the problem so we started looking at SPNs and noticed the QA server had duplicate entries as stated above. Removing the duplicates fixed the issue.