The server collation acts as the default collation for all system databases that are installed with the server, and also any newly created user databases. The server collation is specified during setup

If u want to change the collation u have to rebuilt the master database.

If u dont want to do that then u can do it like this (reinstall sqlserver)

start /wait setup.exe /qb INSTANCENAME=MSSQLSERVER REINSTALL=SQL_Engine REBUILDDATABASE=1 SAPWD=test SQLCOLLATION=SQL_Latin1_General_CP1_CI_AI

from

Killer