Collation issue after update (KB3072779) of SQL Server 2012
I would go and look at the setup.log files for the Service Pack 3 Upgrade. They should be found here:


Each execution of Setup creates log files are created with a new timestamped log folder at %programfiles%\MicrosoftSQL Server\110\Setup Bootstrap\Log\. The time-stamped log folder name format is YYYYMMDD_hhmmss. When Setup is run in an unattended mode, the logs are created at % temp%\sqlsetup*.log. All files in the logs folder are archived into the Log*.cab file in their respective log folder.


More information can be found here: View and Read SQL Server Setup Log Files (Microsoft)

This might provide you with information on what happened.

If you feel like rebuilding you SQL Server instance with the correct collation, then you could try the solution here:

How to change server level collation for a SQL Server Instance

There are slight variations of above post involving re-installing the system databases and or just modifying some objects:  


Changing SQL Server Collation After Installation
Script and Alter SQL Server Database Objects with PowerShell to Correct Collation Issues


It's not highly recommended and is best tested in a non-productive environment first. Currently there are no documented cases of the collation being changed during the setup of a service pack on SQL Server. If you don't find any information in the setup logs, then I would try and contact Microsoft and open a case/ticket.