There is a new Hotfix available for DQS to boost the performance for large datasets (> 1.5 million records): http://support.microsoft.com/kb/2679368/en-us
FIX: Slow performance when you use DQS to perform a data cleansing against a large data source in SQL Server 2012. More info.
Don't forget to run DQSInstaller.exe-Upgrade after installation
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