Performance problems with an ETL refresh can be caused by outdated statistics or bad indexes in the CRM database.  To resolve the issue:

Run the following SQL statements against the CRM database:

1. Exec sp_updatestats
2. EXEC sp_MSforeachtable @command1="print '?' DBCC DBREINDEX ('?', ' ', 80)"
3. Restart SQL server services
4. Run the ETL refresh