Our SQL DBA was in the process of setting up a new SQL server and was having problem authenticating using his domain account. He was able to login using the SA account though. Everything he saw was pointing towards it being a problem with the SPNs for the new server. We looked at the other 3 servers we had and noticed that there were two extra SPN entries for the new server. We used the following commands to remove the SPN entries and then AD authentication worked.
setspn -D MSSQLSvc/SQLServer-FQDN domain\SQLServer
setspn -D MSSQLSvc/SQLServer-FQDN:1433domain\SQLServer
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